diff --git a/src/main/java/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedByOverlap.java b/src/main/java/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedByOverlap.java
new file mode 100644
index 00000000000..9578671163e
--- /dev/null
+++ b/src/main/java/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedByOverlap.java
@@ -0,0 +1,206 @@
+package org.broadinstitute.hellbender.engine;
+
+import htsjdk.samtools.util.Locatable;
+import htsjdk.samtools.util.OverlapDetector;
+import htsjdk.variant.variantcontext.Allele;
+import htsjdk.variant.variantcontext.VariantContext;
+import org.broadinstitute.barclay.argparser.Advanced;
+import org.broadinstitute.barclay.argparser.Argument;
+import org.broadinstitute.hellbender.exceptions.GATKException;
+import org.broadinstitute.hellbender.utils.SimpleInterval;
+import org.broadinstitute.hellbender.utils.Utils;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.stream.Collectors;
+
+
+/**
+ * A MultiVariantWalker that walks over multiple variant context sources in reference order and emits to client tools
+ * groups of all input variant contexts by their start position. This is intended to mimic GATK3 traversal behavior for
+ * some tools.
+ *
+ * As such, the argument '-ignore-variants-starting-outside-interval' has been provided to mimic GATK3's behavior
+ * only presenting variants that start inside the requested interval regardless of whether there is a spanning variant.
+ *
+ * Client tools must implement apply(List<VariantContext> variantContexts, ReferenceContext referenceContext)
+ */
+public abstract class MultiVariantWalkerGroupedByOverlap extends MultiVariantWalker {
+    private List<VariantContext> currentVariants = new ArrayList<>();
+    private String lastCurrentVariantContig;
+    private int lastCurrentVariantEnd;
+    private List<ReadsContext> currentReadsContexts = new ArrayList<>();
+    private OverlapDetector<SimpleInterval> overlapDetector;
+
+    public static final String IGNORE_VARIANTS_THAT_START_OUTSIDE_INTERVAL = "ignore-variants-starting-outside-interval";
+
+    public static final String COMBINE_VARIANTS_DISTANCE = "combine-variants-distance";
+
+    public static final String MAX_COMBINED_DISTANCE = "max-distance";
+
+    public static final String REFERENCE_WINDOW_PADDING = "ref-padding";
+
+    /**
+     * this option has no effect unless intervals are specified.
+     * <p>
+     * This exists to mimic GATK3 interval traversal patterns
+     */
+    @Advanced
+    @Argument(fullName = IGNORE_VARIANTS_THAT_START_OUTSIDE_INTERVAL,
+            doc = "Restrict variant output to sites that start within provided intervals (only applies when an interval is specified)",
+            optional = true)
+    protected boolean ignoreIntervalsOutsideStart = false;
+
+    @Advanced
+    @Argument(fullName = COMBINE_VARIANTS_DISTANCE, doc = "Maximum distance for variants to be grouped together", optional = true)
+    protected int distanceToCombineVariants = defaultDistanceToGroupVariants();
+
+    @Advanced
+    @Argument(fullName = MAX_COMBINED_DISTANCE, doc = "Maximum distance for variants to be grouped together", optional = true)
+    protected int maxCombinedDistance = defaultMaxGroupedSpan();
+
+    @Advanced
+    @Argument(fullName = REFERENCE_WINDOW_PADDING, doc = "Number of bases on either side to expand spanning reference window", optional = true)
+    protected int referenceWindowPadding = defaultReferenceWindowPadding();
+
+    @Advanced
+    @Argument(fullName = "ignore-reference-blocks", shortName = "ignore-ref-blocks", optional = true)
+    protected boolean ignoreReferenceBlocks = false;
+
+    // override to group variants that start nearby but not at the same locus
+    protected int defaultDistanceToGroupVariants() {
+        return 10000;
+    }
+
+    // override to change reference padding
+    protected int defaultReferenceWindowPadding() {
+        return 1;
+    }
+
+    // override to cap the size span of combined variants
+    protected int defaultMaxGroupedSpan() {
+        return Integer.MAX_VALUE;
+    }
+
+    @Override
+    public boolean requiresReference() {
+        return true;
+    }
+
+    /**
+     * This method keeps track of all the variants it is passed and will feed all the variants that start at the same
+     * site to the reduce method.
+     *
+     * {@inheritDoc}
+     */
+    @Override
+    public final void apply(VariantContext variant, ReadsContext readsContext, ReferenceContext referenceContext, FeatureContext featureContext) {
+
+        // Filtering out variants that start outside of the specified intervals
+        if (ignoreIntervalsOutsideStart && !isWithinInterval(new SimpleInterval(variant.getContig(), variant.getStart(), variant.getStart()))) {
+            return;
+        }
+
+        if (ignoreReferenceBlocks && variant.getAlternateAlleles().size() ==1 && variant.getAlternateAllele(0).equals(Allele.NON_REF_ALLELE)) {
+            return;
+        }
+
+        // Collecting all the reads that start at a particular base into one.
+        if (currentVariants.isEmpty()) {
+            lastCurrentVariantContig = variant.getContig();
+        } else if (!currentVariants.get(0).contigsMatch(variant)
+                || variant.getStart() > lastCurrentVariantEnd) {
+            // Emptying any sites which should emit a new VC since the last one
+            apply(new ArrayList<>(currentVariants), currentReadsContexts);
+            currentVariants.clear();
+            currentReadsContexts.clear();
+        }
+
+        currentVariants.add(variant);
+        currentReadsContexts.add(readsContext);
+        if (variant.getEnd() > lastCurrentVariantEnd || !lastCurrentVariantContig.equals(variant.getContig())) {
+            lastCurrentVariantEnd = variant.getEnd();
+            lastCurrentVariantContig = variant.getContig();
+        }
+    }
+
+    /**
+     * This method must be implemented by tool authors.
+     *
+     * This is the primary traversal for any MultiVariantWalkerGroupedOnStart walkers. Will traverse over input variant contexts
+     * and call #apply() exactly once for each unique reference start position. All variants starting at each locus
+     * across source files will be grouped and passed as a list of VariantContext objects.
+     *  @param variantContexts  VariantContexts from driving variants with matching start position
+     *                         NOTE: This will never be empty
+     * @param referenceContext  ReferenceContext object covering the reference of the longest spanning VariantContext
+     * @param readsContexts
+     */
+    public abstract void apply(final List<VariantContext> variantContexts, final ReferenceContext referenceContext, final List<ReadsContext> readsContexts);
+
+    public void apply(List<VariantContext> variantContexts, final List<ReadsContext> readsContexts) {
+        apply(variantContexts, makeSpanningReferenceContext(variantContexts, referenceWindowPadding), readsContexts);
+    }
+
+    /**
+     * Helper method that ensures the reference context it returns is adequate to span the length of all the accumulated
+     * VariantContexts. It assumes that all variant contexts in currentVariants have the same contig.
+     */
+    private ReferenceContext makeSpanningReferenceContext(final List<VariantContext> variantContexts, final int referenceWindowPadding) {
+        Utils.nonEmpty(variantContexts, "Must have at least one current variant context");
+        final List<String> contigs = variantContexts.stream().map(VariantContext::getContig).distinct().collect(Collectors.toList());
+        Utils.validate(contigs.size() == 1, "variant contexts should all have the same contig");
+        final int minStart = variantContexts.stream().mapToInt(VariantContext::getStart).min().getAsInt();
+        final int maxEnd = variantContexts.stream().mapToInt(VariantContext::getEnd).max().getAsInt();
+        final SimpleInterval combinedInterval = new SimpleInterval(contigs.get(0), minStart, maxEnd);
+
+        final ReferenceContext combinedReferenceContext = new ReferenceContext(reference, combinedInterval);
+        combinedReferenceContext.setWindow(referenceWindowPadding,referenceWindowPadding);
+        return combinedReferenceContext;
+    }
+
+    /**
+     * {@inheritDoc}
+     *
+     * Implementation of multi-variant grouped on start traversal.
+     *
+     * NOTE: You should only override {@link #traverse()} if you are writing a new walker base class in the
+     * engine package that extends this class. It is not meant to be overridden by tools outside of the
+     * engine package.
+     */
+    @Override
+    public void traverse() {
+        beforeTraverse();
+        super.traverse();
+        afterTraverse();
+    }
+
+    /**
+     * Marked final so that tool authors don't override it. Tool authors should override {@link #onTraversalStart} instead.
+     */
+    private void beforeTraverse() {
+        overlapDetector = hasUserSuppliedIntervals() ? OverlapDetector.create(intervalArgumentCollection.getIntervals(getBestAvailableSequenceDictionary())) : null;
+    }
+
+    /**
+     * @param loc locatable to query
+     * @return true if the query loc is entirely contained by the interval, true if no interval
+     */
+    protected final boolean isWithinInterval(Locatable loc) {
+        return (overlapDetector==null || overlapDetector.overlapsAny(loc));
+    }
+
+    /**
+     * Clear accumulated reads before {@link #onTraversalSuccess()} is accessed
+     */
+    private void afterTraverse() {
+        // Clearing the accumulator
+        if (currentVariants.isEmpty()) {
+            logger.warn("Error: The requested interval contained no data in source VCF files");
+
+        } else {
+            apply(currentVariants, currentReadsContexts);
+        }
+    }
+}
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/AnnotationUtils.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/AnnotationUtils.java
index 7ba0a0baa24..f979b38dc9c 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/AnnotationUtils.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/AnnotationUtils.java
@@ -6,10 +6,12 @@
 import org.apache.commons.lang3.StringUtils;
 import htsjdk.variant.vcf.VCFHeaderLineCount;
 import htsjdk.variant.vcf.VCFInfoHeaderLine;
+import htsjdk.variant.vcf.VCFConstants;
 import org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.*;
 import org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods;
 import org.broadinstitute.hellbender.utils.read.GATKRead;
 import org.broadinstitute.hellbender.utils.variant.GATKVCFHeaderLines;
+import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants;
 
 import java.util.*;
 
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF.java
index ef416e726b7..073b43fa0aa 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF.java
@@ -487,7 +487,7 @@ private boolean isMonomorphicCallWithAlts(final VariantContext result) {
         final Genotype genotype = result.getGenotype(0);
         return (hasGenotypeValuesArray(posteriorsKey, genotype)
                 && (genotype.isHomRef() || isNoCalledHomRef(posteriorsKey, genotype) || (genotype.hasPL() && MathUtils.minElementIndex(genotype.getPL()) == 0))
-                && result.getAlternateAlleles().stream().anyMatch(this::isConcreteAlt));
+                && result.getAlternateAlleles().stream().anyMatch(GATKVariantContextUtils::isConcreteAlt));
     }
 
     /**
@@ -526,26 +526,13 @@ boolean shouldBeReblocked(final VariantContext vc) {
 
         final List<Allele> finalAlleles = alleleCounts.asAlleleList(vc.getAlleles());
         return (pls != null && pls[0] < rgqThreshold)
-                || !genotypeHasConcreteAlt(finalAlleles)
+                || !GATKVariantContextUtils.genotypeHasConcreteAlt(finalAlleles)
                 || finalAlleles.stream().anyMatch(a -> a.equals(Allele.NON_REF_ALLELE))
                 || (!genotype.hasPL() && !genotype.hasGQ()
                 // If TREE_SCORE threshold is set to be > 0 then sites without TREE_SCORE should be reblocked.
                 || vc.getAttributeAsDouble(GATKVCFConstants.TREE_SCORE, 0) < treeScoreThreshold);
     }
 
-    /**
-     * Is there a real ALT allele that's not <NON_REF> or * ?
-     * @param alleles   alleles in the called genotype
-     * @return true if the genotype has a called allele that is a "real" alternate
-     */
-    private boolean genotypeHasConcreteAlt(final List<Allele> alleles) {
-        return alleles.stream().anyMatch(this::isConcreteAlt);
-    }
-
-    private boolean isConcreteAlt(final Allele a) {
-        return !a.isReference() && !a.isSymbolic() && !a.equals(Allele.SPAN_DEL);
-    }
-
     /**
      * "reblock" a variant by converting its genotype to homRef, changing PLs, adding reblock END tags and other attributes
      * @param lowQualityVariant  a variant already determined to be low quality
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/VCFComparator.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/VCFComparator.java
new file mode 100644
index 00000000000..494f9a42857
--- /dev/null
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/VCFComparator.java
@@ -0,0 +1,903 @@
+package org.broadinstitute.hellbender.tools.walkers.variantutils;
+
+import htsjdk.variant.variantcontext.*;
+import htsjdk.variant.vcf.VCFConstants;
+import org.apache.commons.collections4.CollectionUtils;
+import org.broadinstitute.barclay.argparser.*;
+import org.broadinstitute.hellbender.engine.*;
+import org.broadinstitute.hellbender.exceptions.UserException;
+import org.broadinstitute.hellbender.tools.walkers.annotator.*;
+import org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_StandardAnnotation;
+import org.broadinstitute.hellbender.tools.walkers.genotyper.AlleleSubsettingUtils;
+import org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAssignmentMethod;
+import org.broadinstitute.hellbender.utils.MathUtils;
+import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants;
+import org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils;
+import picard.cmdline.programgroups.VariantEvaluationProgramGroup;
+
+import java.io.PrintStream;
+import java.util.*;
+import java.util.stream.Collectors;
+
+/**
+ * A tool to allow for comparison of two single-sample GVCFs or multi-sample VCFs when some differences are expected
+ * input variants should be tagged "actual" or "expected"
+ *
+ * Example usage:
+ * java -jar gatk.jar VCFComparator -R ref.fasta -V:actual actual.vcf -V:expected expected.vcf
+ *
+ * Caveats:
+ * Reference blocks are not checked
+ * VCFComparator will ignore version-specific NaN versus empty AS_RAW annotation discrepancies
+ * VCFs are both expected to NOT have split multi-alleleics
+ */
+@ExperimentalFeature
+@CommandLineProgramProperties(
+        summary = "Compare two VCFs, as for pipeline test updates",
+        oneLineSummary = "Compare two VCFs",
+        programGroup = VariantEvaluationProgramGroup.class
+)
+public class VCFComparator extends MultiVariantWalkerGroupedByOverlap {
+    public static final String ALLOW_NEW_STARS_LONG_NAME = "allow-new-stars";
+    public static final String IGNORE_QUALS_LONG_NAME = "ignore-quals";
+    public static final String DP_CHANGE_ALLOWED_LONG_NAME = "dp-change-allowed";
+    public static final String RANK_SUM_CHANGE_ALLOWED_LONG_NAME = "ranksum-change-allowed";
+    public static final String POSITIONS_ONLY_LONG_NAME = "positions-only";
+
+    private VariantAnnotatorEngine annotatorEngine;
+    private boolean isSingleSample = true;
+    private boolean alleleNumberIsDifferent = false;
+    private boolean inbreedingCoeffIsDifferent = false;
+    private final List<String> annotationsThatVaryWithNoCalls = Arrays.asList(VCFConstants.ALLELE_NUMBER_KEY, GATKVCFConstants.INBREEDING_COEFFICIENT_KEY,
+            GATKVCFConstants.AS_INBREEDING_COEFFICIENT_KEY, GATKVCFConstants.EXCESS_HET_KEY,
+            GATKVCFConstants.MLE_ALLELE_COUNT_KEY, GATKVCFConstants.MLE_ALLELE_FREQUENCY_KEY, VCFConstants.ALLELE_FREQUENCY_KEY,
+            VCFConstants.DEPTH_KEY, GATKVCFConstants.QUAL_BY_DEPTH_KEY, GATKVCFConstants.AS_QUAL_BY_DEPTH_KEY,
+            GATKVCFConstants.VQS_LOD_KEY, GATKVCFConstants.AS_VQS_LOD_KEY, GATKVCFConstants.AS_FILTER_STATUS_KEY,
+            GATKVCFConstants.CULPRIT_KEY, GATKVCFConstants.AS_CULPRIT_KEY); //AC should be the same
+    private boolean failOnCompletion = false;
+
+    @Argument(fullName = "warn-on-errors",
+            shortName = "warn-on-errors",
+            doc = "just emit warnings on errors instead of terminating the run at the first instance. Won't fail unless --finish-before-failing is set",
+            optional = true)
+    private boolean warnOnError = false;
+
+    @Argument(fullName = "finish-before-failing",
+    doc = "emit warnings as necesarry, but perform the whole comparison before failing",
+    optional= true)
+    private boolean finishBeforeFailing = false;
+
+    @Argument(fullName = "default-ploidy", optional = true, doc = "Overall expected ploidy. Default value is 2.")
+    private int defaultPloidy = 2;
+
+    @Argument(fullName = IGNORE_QUALS_LONG_NAME, optional = true, mutex={POSITIONS_ONLY_LONG_NAME})
+    private boolean ignoreQuals = false;
+
+    @Argument(fullName = "qual-change-allowed", optional = true)
+    private double qualTolerance = 0.001;
+
+    @Argument(fullName = "inbreeding-coeff-change-allowed", optional = true)
+    private double inbreedingCoeffTolerance = 0.001;
+
+    @Argument(fullName = "good-qual-threshold", optional = true, doc = "Variants with QUAL at or above this value are considered high quality and should appear in both files")
+    private double goodQualThreshold = 100.0;
+
+    @Argument(fullName = DP_CHANGE_ALLOWED_LONG_NAME, optional = true, doc = "Note that this is a signed change (actual - expected)", mutex={POSITIONS_ONLY_LONG_NAME})
+    private int dpChange = 0;
+
+    @Argument(fullName = RANK_SUM_CHANGE_ALLOWED_LONG_NAME, optional = true, doc = "Amount of numerical 'noise' allowed in rank sum annotations")
+    private double ranksumTolerance = 0.0;
+
+    @Argument(fullName = "likelihood-change-allowed", optional = true)
+    private int likelihoodTolerance = 0;
+
+    @Argument(fullName = "ignore-non-ref-data", optional = true)
+    private boolean ignoreNonRefData = false;
+
+    @Argument(fullName = "ignore-annotations", optional = true, doc = "Only match on position and alleles, ignoring all INFO annotations", mutex={POSITIONS_ONLY_LONG_NAME})
+    private boolean ignoreAnnotations = false;
+
+    @Argument(fullName = "ignore-genotype-annotations", optional = true, doc = "Only match on genotype call, ignoring all FORMAT annotations", mutex={POSITIONS_ONLY_LONG_NAME})
+    private boolean ignoreGenotypeAnnotations = false;
+
+    @Argument(fullName = "ignore-genotype-phasing", optional = true, doc = "Only check called genotype alleles, not order or phasing status")
+    private boolean ignoreGenotypePhasing = false;
+
+    @Argument(fullName = "ignore-filters", optional = true, doc = "Ignore filter status when comparing variants", mutex={POSITIONS_ONLY_LONG_NAME})
+    private boolean ignoreFilters = false;
+
+    @Argument(fullName = "ignore-attribute", optional = true, doc = "Ignore INFO attributes with this key", mutex={POSITIONS_ONLY_LONG_NAME})
+    private List<String> ignoreAttributes = new ArrayList<>(5);
+
+    @Argument(fullName = POSITIONS_ONLY_LONG_NAME, optional = true, doc = "Only match on position, ignoring alleles and annotations", mutex={})
+    private boolean positionsOnly = false;
+
+    @Argument(fullName = ALLOW_NEW_STARS_LONG_NAME, optional = true, doc = "Allow additional * alleles in actual if there is a corresponding deletion", mutex={POSITIONS_ONLY_LONG_NAME})
+    private boolean allowNewStars = false;
+
+    @Argument(fullName = "allow-extra-alleles", optional = true, doc = "Allow extra alleles in actual provided actual is a superset of expected", mutex={ALLOW_NEW_STARS_LONG_NAME, POSITIONS_ONLY_LONG_NAME})
+    private boolean allowExtraAlleles = false;
+
+    @Argument(fullName = "allow-missing-stars", optional = true, doc = "Allow missing * in actual if actual has no corresponding deletions")
+    private boolean allowMissingStars = false;
+
+    @Argument(fullName = "ignore-star-attributes", optional = true, doc = "Ignore annotation values for spanning deletion (*) alleles")
+    private boolean ignoreStarAttributes = false;
+
+    @Argument(fullName = "allow-nan-mismatch", optional = true, doc = "Allow VCF values of missing (.) and NaN to match")
+    private boolean allowNanMismatch = false;
+
+    @Argument(fullName = "mute-acceptable-diffs", optional = true, doc = "Suppress warnings or exceptions for differences that are consequences of low quality genotypes or AN discrepancies")
+    private boolean muteDiffs = false;
+
+    @Argument(fullName = "ignore-hom-ref-attributes", optional = true, doc = "Skip attribute comparison for homozygous reference genotypes")
+    private boolean ignoreHomRefAttributes = false;
+
+    @Argument(fullName = "ignore-dbsnp-ids", optional = true)
+    private boolean ignoreDbsnp = false;
+
+    @Advanced
+    @Argument(fullName=ReblockGVCF.ANNOTATIONS_TO_KEEP_LONG_NAME, doc="Annotations that are not recognized by GATK that should be checked, otherwise they are removed if ignore-non-ref-data is set.", optional = true)
+    private List<String> annotationsToKeep = new ArrayList<>();
+
+    @Hidden
+    @Argument(fullName = "output-warnings", optional = true, doc = "Output warnings to a file, useful for testing")
+    private GATKPath warningsOutput = null;
+
+    private PrintStream outputStream = null;
+
+    @Override
+    public boolean doDictionaryCrossValidation() {
+        return false;
+    }  //speed things up a bit
+
+    @Override
+    public boolean useVariantAnnotations() { return true;}
+
+    @Override
+    public List<Class<? extends Annotation>> getDefaultVariantAnnotationGroups() {
+        return Arrays.asList(StandardAnnotation.class, AS_StandardAnnotation.class);
+    }
+
+    @Override
+    public void onTraversalStart() {
+        if (getDrivingVariantsFeatureInputs().size() != 2) {
+            throw new UserException.BadInput("VCFComparator expects exactly two inputs -- one actual and one expected.");
+        }
+        final List<FeatureInput<VariantContext>> expected = getDrivingVariantsFeatureInputs().stream().filter(file -> file.getName().equals("expected")).collect(Collectors.toList());
+        if (expected.size() != 1) {
+            throw new UserException.BadInput("Tool requires exactly one expected input file");
+        }
+
+        annotatorEngine = new VariantAnnotatorEngine(makeVariantAnnotations(), null, Collections.emptyList(), false, false);
+
+        isSingleSample = getSamplesForVariants().size() == 1 ? true : false;  //if either expected or actual has more than one sample then we're not single-sample
+
+        if (warningsOutput != null) {
+            outputStream = new PrintStream(warningsOutput.getOutputStream());
+        }
+    }
+
+    @Override
+    public void apply(final List<VariantContext> variantContexts, final ReferenceContext referenceContext, final List<ReadsContext> readsContexts) {
+        if (isSingleSample && !variantContexts.get(0).getAlleles().contains(Allele.NON_REF_ALLELE)) {
+            throw new UserException.BadInput("Single-sample mode expects two GVCFs with <NON_REF> data for comparison");
+        }
+
+        if (variantContexts.size() == 1) {
+            final VariantContext vc = variantContexts.get(0);
+            //TODO: if there's a variant that overlaps the requested interval the start may not be in the requested intervals
+            if (!muteDiffs) {
+                throwOrWarn(new UserException("Unmatched variant in " + vc.getSource() + " at position " + vc.getContig() + ":" + vc.getStart()));
+            //low coverage sites will have QUAL for singleton hom-vars boosted because of GQ0 hom-refs
+            } else if (hasGoodEvidence(vc)) {
+                throwOrWarn(new UserException("Unmatched variant in " + vc.getSource() + " at position " + vc.getContig() + ":" + vc.getStart()));
+            }
+        }
+
+        //here we have all variants overlapping a given position
+        //if there's no actual for the expected (at the same position), see if the expected has an overlapping deletion
+        for (final VariantContext vc : variantContexts) {
+            if (vc.getSource().equals("actual")) {  //there may be more expected than actual variants, but only compare once
+                continue;  //TODO: this means we don't report cases where actual has multiple reference blocks spanning expected as unmatched
+            }
+            //vc is guaranteed to be from expected
+
+            //variantContexts can have a bunch of overlapping variants, but use the start position to compare. Could still have two alleles with same start.
+            final List<VariantContext> matches = variantContexts.stream().filter(v -> v.getStart() == vc.getStart()).collect(Collectors.toList());
+            //matches includes vc (both actual and expected)
+            //TODO: matches.size() can be up to 2 times the number of haplotypes (based on ploidy). So checking only one match won't work for non-diploid organisms
+            if (matches.size() == 1 ) {
+                // if there's only one match, then it's the expected matching itself, so actual is missing the same vc start
+                // if it's a high quality site, throw an error/warning otherwise it's low quality so skip it
+                if (isHighQuality(vc) && hasGoodEvidence(vc)
+                        && !vc.getGenotype(0).getAlleles().contains(Allele.SPAN_DEL)){
+                    throwOrWarn(new UserException("Apparent unmatched high quality variant in " + vc.getSource() + " at " + vc.getContig() + ":" + vc.getStart()));
+                } else {
+                    return;
+                }
+            } else {
+                if ((!isHighQuality(vc) || (isSingleSample && !GATKVariantContextUtils.genotypeHasConcreteAlt(vc.getGenotype(0).getAlleles())))
+                && ignoreHomRefAttributes) {
+                    return;
+                }
+                final VariantContext match;
+                // VCFs are expected to NOT have split multi-alleleics
+                if (!matches.get(0).getSource().equals(vc.getSource())) {
+                    match = matches.get(0);
+                } else {
+                    match = matches.get(1);
+                }
+
+                final List<VariantContext> overlappingDels = variantContexts.stream().filter(v -> v.getStart() < vc.getStart() && v.overlaps(vc))
+                        .collect(Collectors.toList());
+
+                final VariantContext expectedTrimmed = trimAlleles(vc, overlappingDels);
+                final VariantContext actualTrimmed = trimAlleles(match, overlappingDels);
+
+                //do single-sample GVCF checks, including deletion trimming and dropping
+                if (isSingleSample) {
+                    try {
+                        validateSingleSampleDeletions(vc, match, expectedTrimmed, actualTrimmed, overlappingDels);
+                    } catch (UserException e) {
+                        throwOrWarn(e);
+                    }
+                }
+
+                if (positionsOnly) {
+                    return;
+                }
+
+                //more rigorous checks on annotations and genotypes
+                try {
+                    checkVariantContextsAreMatching(actualTrimmed, expectedTrimmed, overlappingDels);
+                } catch (UserException e) {
+                    final boolean hasLowQualityGenotype = expectedTrimmed.getGenotypes().stream().anyMatch(g -> g.getGQ() < 20);
+                     if (!muteDiffs || !(alleleNumberIsDifferent || inbreedingCoeffIsDifferent || hasLowQualityGenotype)) {
+                        throwOrWarn(e);
+                    }
+                }
+
+                if (alleleNumberIsDifferent && !muteDiffs) {
+                    logger.warn("Observed allele number differed at position " + vc.getContig() + ":" + vc.getStart());
+                }
+                if (inbreedingCoeffIsDifferent && expectedTrimmed.getGenotypes().stream().anyMatch(g -> g.getGQ() < 20) && !muteDiffs) {
+                    logger.warn("Low quality genotype may have caused inbreeding coeff differences at position " + vc.getContig() + ":" + vc.getStart());
+                }
+            }
+        }
+    }
+
+    private void validateSingleSampleDeletions(final VariantContext vc, final VariantContext match,
+                                               final VariantContext expectedTrimmed, final VariantContext actualTrimmed,
+                                               final List<VariantContext> overlappingDels) {
+        final Genotype expectedGenotype = expectedTrimmed.getGenotype(0);
+        final List<Allele> expectedGenotypeAlleles = expectedGenotype.getAlleles();
+        final Genotype actualGenotype = actualTrimmed.getGenotype(0);
+        final List<Allele> actualGenotypeAlleles = actualGenotype.getAlleles();
+
+        if (ignoreGenotypePhasing && !actualHasNewAlleles(expectedTrimmed, actualTrimmed)) {
+            return;
+        }
+
+        // make sure both genotypes are not haploid and do use order here so we can check phasing
+        if (!expectedGenotypeAlleles.get(0).equals(actualGenotypeAlleles.get(0)) || ( expectedGenotypeAlleles.size() > 1 && actualGenotypeAlleles.size() > 1 && !expectedGenotypeAlleles.get(1).equals(actualGenotypeAlleles.get(1)))) {
+            if (expectedGenotype.isPhased() && expectedGenotypeAlleles.get(1).equals(actualGenotypeAlleles.get(0)) && expectedGenotypeAlleles.get(0).equals(actualGenotypeAlleles.get(1))) {
+                throw wrapWithPosition(vc.getContig(), vc.getStart(), new UserException("phasing is swapped. Actual in phaseset "
+                        + actualGenotype.getExtendedAttribute(GATKVCFConstants.HAPLOTYPE_CALLER_PHASING_ID_KEY, "") + " has "
+                        + actualGenotype.getGenotypeString(false)
+                        + " expected in phaseset " + expectedGenotype.getExtendedAttribute(GATKVCFConstants.HAPLOTYPE_CALLER_PHASING_ID_KEY, "")
+                        +" has " + expectedGenotype.getGenotypeString(false)));
+            }
+            if (overlappingDels.size() == 0) {
+                throw wrapWithPosition(vc.getContig(), vc.getStart(), makeGenotypeExceptionFromDifference("called genotype alleles",
+                        actualGenotype.getGenotypeString(false),
+                        expectedGenotype.getGenotypeString(false)));
+            }
+
+            //this is okay if a star got corrected by dropping an upstream hom ref del
+            //could be dropped hom ref
+            if (overlappingDels.stream().anyMatch(v -> v.getGenotype(0).isHomRef())) {
+                try {
+                    checkAttributes(vc.getAttributes(), match.getAttributes(), vc.getAlleles(), match.getAlleles(), vc.getPhredScaledQual());
+                } catch (UserException e) {
+                    throw wrapWithPosition(vc.getContig(), vc.getStart(), new UserException("INFO attributes do not match at " + vc.getContig() + ":" + vc.getStart()));
+                }
+                try {
+                    checkGenotypes(expectedGenotype, actualGenotype);
+                } catch (final UserException e) {
+                    throw wrapWithPosition(vc.getContig(), vc.getStart(), e);
+                }
+            } else if (overlappingDels.size() == 0 && expectedGenotypeAlleles.contains(Allele.SPAN_DEL) && !actualGenotypeAlleles.contains(Allele.SPAN_DEL)) {
+                return;
+            } else {
+                if (overlappingDels.stream().anyMatch(v -> v.getSource().equals("actual"))) {  //there should be one overlapping that got trimmed and the other shouldn't overlap anymore
+                    if (!allowMissingStars) {
+                        throw wrapWithPosition(vc.getContig(), vc.getStart(), new UserException("genotype alleles do not match at spanning deletion site. "
+                                +  vc.getSource() + " has " + expectedGenotype.toString() + " and " + match.getSource() + " has "
+                                + actualGenotype.toString()));
+                    }
+                    return;
+                } else {
+                    final VariantContext overlapper = overlappingDels.get(0);
+                    final VariantContext trimmedOverlapper = trimAlleles(overlapper, overlappingDels);
+                    if (overlapper.overlaps(vc) && !trimmedOverlapper.overlaps(vc)) {
+                        return;
+                    }
+                }
+
+            }
+        }
+    }
+
+    private boolean hasGoodEvidence(final VariantContext vc) {
+        return (vc.getPhredScaledQual() > goodQualThreshold)
+            && (vc.getAttributeAsInt(VCFConstants.DEPTH_KEY,0)/(double)vc.getAttributeAsInt(VCFConstants.ALLELE_NUMBER_KEY,0)) > 5
+                && vc.getGenotypes().stream().filter(g -> !g.isHomRef()).mapToInt(Genotype::getGQ).sum() > goodQualThreshold;
+    }
+
+    private void checkVariantContextsAreMatching(final VariantContext actual, final VariantContext expected,
+                                                 final List<VariantContext> overlappingDels) {
+        if (!actual.getContig().equals(expected.getContig())) {
+            throw wrapWithPosition(expected.getContig(), expected.getStart(), new UserException("contigs differ for VCs"));
+        }
+
+        if (actual.getStart() != expected.getStart()) {
+            throw wrapWithPosition(expected.getContig(), expected.getStart(), new UserException("start positions differ for VCs"));
+        }
+
+        //don't check end in case we're being lenient about alleles
+
+        //check alleles
+        if (actualHasNewAlleles(expected, actual)) {
+            try {
+                checkAlleles(actual, expected, overlappingDels);
+            } catch (final UserException e) {
+                throw wrapWithPosition(expected.getContig(), expected.getStart(), e);
+            }
+        }
+
+        if (!ignoreDbsnp && !actual.getID().equals(expected.getID())) {  //more alleles might mean more dbSNP matches
+            throw wrapWithPosition(expected.getContig(), expected.getStart(), new UserException("dbsnp IDs differ for VCs"));
+        }
+
+        if (ignoreAnnotations) {
+            return;
+        }
+
+        if (!ignoreQuals) {
+            final double diff = Math.abs(actual.getPhredScaledQual() - expected.getPhredScaledQual());
+            if (diff > qualTolerance) {
+                throw wrapWithPosition(expected.getContig(), expected.getStart(), new UserException("qual scores differ by " + diff + ", which is more than " + qualTolerance));
+            }
+        }
+
+        try {
+            checkAttributes(actual.getAttributes(), expected.getAttributes(), actual.getAlternateAlleles(), expected.getAlternateAlleles(), expected.getPhredScaledQual());
+        } catch (final UserException e) {
+            throw wrapWithPosition(expected.getContig() ,expected.getStart() , e);
+        }
+
+        if (!alleleNumberIsDifferent) {
+            if (!ignoreFilters) {
+                if (actual.filtersWereApplied() != expected.filtersWereApplied()) {
+                    throw wrapWithPosition(expected.getContig(), expected.getStart(), new UserException(" filters were not applied to both variants"));
+                }
+                if (!actual.getFilters().equals(expected.getFilters())) {
+                    throw wrapWithPosition(expected.getContig(), expected.getStart(), new UserException("variants have different filters: expected has "
+                    + (expected.getFilters().isEmpty() ? "PASS" : expected.getFilters()) + " and actual has " + actual.getFilters()));
+                }
+            }
+
+            for (int i = 0; i < actual.getGenotypes().size(); i++) {
+                try {
+                    checkGenotypes(actual.getGenotype(0), expected.getGenotype(0));
+                } catch (final UserException e) {
+                    throw wrapWithPosition(expected.getContig(), expected.getStart(), e);
+                }
+            }
+        }
+    }
+
+    private void checkAlleles(final VariantContext actual, final VariantContext expected, final List<VariantContext> overlappingDels) {
+        //TODO: this could be more rigorous
+        if (ignoreGenotypePhasing && !actualHasNewAlleles(actual, expected)) {
+            return;
+        }
+        if (!allowExtraAlleles && actualHasNewAlleles(actual, expected)) {
+            throw new UserException("Alleles are mismatched at " + actual.getContig() + ":" + actual.getStart() + ": actual has "
+                    + actual.getAlternateAlleles() + " and expected has " + expected.getAlternateAlleles());
+
+        } else if (!allowNewStars && hasNewStar(actual, expected)) {
+            if (overlappingDels.size() == 0 || !overlappingDels.stream().anyMatch(vc -> vc.getSource().equals("actual"))) {
+                throw new UserException("Actual has new unmatched * allele. Alleles are mismatched at " + actual.getContig() + ":" + actual.getStart() + ": actual has "
+                        + actual.getAlternateAlleles() + " and expected has " + expected.getAlternateAlleles());
+            }
+            //this is a GenomicsDB/CombineGVCFs bug -- there is an overlapping deletion and * should be output, but those tools don't account for multiple haplotypes and upstream variant "ends" the deletion
+        } else if (!allowMissingStars && hasMissingStar(actual, expected)) {
+            final Set<Allele> remainder = new LinkedHashSet<>(expected.getAlleles());
+            remainder.removeAll(actual.getAlleles());
+            if (remainder.size() > 1 || !remainder.contains(Allele.SPAN_DEL)) {
+                throw new UserException("Actual missing * allele. Alleles are mismatched at " + actual.getContig() + ":" + actual.getStart() + ": actual has "
+                        + actual.getAlternateAlleles() + " and expected has " + expected.getAlternateAlleles());
+            }
+        } else {
+            throw new UserException("Alleles are mismatched at " + actual.getContig() + ":" + actual.getStart() + ": actual has "
+                    + actual.getAlternateAlleles() + " and expected has " + expected.getAlternateAlleles());
+        }
+    }
+
+    /**
+     * Compare VC alternate alleles
+     * @param actual
+     * @param expected
+     * @return
+     */
+    private boolean actualHasNewAlleles(final VariantContext actual, final VariantContext expected) {
+        return !actual.getAlternateAlleles().stream().allMatch(a -> GATKVariantContextUtils.isAlleleInList(
+                actual.getReference(), a, expected.getReference(), expected.getAlternateAlleles()));
+    }
+
+    private boolean hasMissingStar(final VariantContext actual, final VariantContext expected) {
+        return expected.getAlleles().contains(Allele.SPAN_DEL) && !actual.getAlleles().contains(Allele.SPAN_DEL);
+    }
+
+    private boolean hasNewStar(final VariantContext actual, final VariantContext expected) {
+        return actual.getAlleles().contains(Allele.SPAN_DEL) && !expected.getAlleles().contains(Allele.SPAN_DEL);
+    }
+
+    private UserException wrapWithPosition(final String contig, final int start, final UserException e) {
+        return new UserException("At position " + contig + ":" +start + " " + e.getMessage());
+    }
+
+    @SuppressWarnings("unchecked")
+    private void checkAttributes(final Map<String, Object> actual, final Map<String, Object> expected,
+                                 final List<Allele> actualAlts, final List<Allele> expectedAlts,
+                                 final double expectedQual) {
+        final Set<String> expectedKeys = new LinkedHashSet<>(expected.keySet());
+
+        //do a precheck on AN because then we can't expect the rest of the annotations to match
+        alleleNumberIsDifferent = actual.containsKey(VCFConstants.ALLELE_NUMBER_KEY) && !isAttributeValueEqual(VCFConstants.ALLELE_NUMBER_KEY, actual.get(VCFConstants.ALLELE_NUMBER_KEY),
+                    expected.get(VCFConstants.ALLELE_NUMBER_KEY));
+
+        if (actual.containsKey(GATKVCFConstants.INBREEDING_COEFFICIENT_KEY)) {
+            try {
+                inbreedingCoeffIsDifferent = !isAttributeEqualDoubleSmart(GATKVCFConstants.INBREEDING_COEFFICIENT_KEY,
+                        Double.parseDouble(actual.get(GATKVCFConstants.INBREEDING_COEFFICIENT_KEY).toString()),
+                        Double.parseDouble(expected.get(GATKVCFConstants.INBREEDING_COEFFICIENT_KEY).toString()), 0.001);
+            } catch (UserException e) {
+                inbreedingCoeffIsDifferent = true;
+                throw e;
+            }
+        }
+
+        if (actual.containsKey(GATKVCFConstants.AS_INBREEDING_COEFFICIENT_KEY) && !(actual.get(GATKVCFConstants.AS_INBREEDING_COEFFICIENT_KEY) instanceof List)) {
+            try {
+                inbreedingCoeffIsDifferent = !isAttributeEqualDoubleSmart(GATKVCFConstants.AS_INBREEDING_COEFFICIENT_KEY,
+                        Double.parseDouble(actual.get(GATKVCFConstants.AS_INBREEDING_COEFFICIENT_KEY).toString()),
+                        Double.parseDouble(expected.get(GATKVCFConstants.AS_INBREEDING_COEFFICIENT_KEY).toString()), 0.001);
+            } catch (final UserException e) {
+                inbreedingCoeffIsDifferent = true;
+                throw e;
+            }
+        }
+
+        for (final Map.Entry<String, Object> exp : expected.entrySet()) {
+            final Object expectedValue = exp.getValue();
+            final String key = exp.getKey();
+            if (actual.containsKey(key) && actual.get(key) != null) {
+                //we already checked these
+                if (key.equals(GATKVCFConstants.INBREEDING_COEFFICIENT_KEY)
+                        || key.equals(VCFConstants.ALLELE_NUMBER_KEY)
+                        || (key.equals(GATKVCFConstants.AS_INBREEDING_COEFFICIENT_KEY) && !(expected.get(key) instanceof List))
+                        || ignoreAttributes.contains(key)) {
+                    continue;
+                }
+                final Object actualValue = actual.get(key);
+                if (expectedValue instanceof List && actualValue instanceof List || key.equals(GATKVCFConstants.AS_SB_TABLE_KEY)) {
+                    // both values are lists, compare element by element
+                    final List<? extends Object> expectedList, actualList;
+                    if (key.contains("AS_") || key.equals(GATKVCFConstants.AS_SB_TABLE_KEY)) {
+                        expectedList = AnnotationUtils.decodeAnyASListWithRawDelim(expectedValue.toString());
+                        actualList = AnnotationUtils.decodeAnyASListWithRawDelim(actualValue.toString());
+                    } else {
+                        expectedList = (List<Object>) expectedValue;
+                        actualList = (List<Object>) actualValue;
+                    }
+                    if (actualList.size() != expectedList.size() && !key.contains("AS_")) {  //TODO: account for subset alleles
+                        throw makeVariantExceptionFromDifference("attributes", actual.keySet().toString(),
+                                expected.keySet().toString());
+                    }
+                    final List<? extends Object> expectedListCommon, actualListCommon;
+                    if (key.equals(VCFConstants.ALLELE_COUNT_KEY) || key.equals(GATKVCFConstants.MLE_ALLELE_COUNT_KEY)) {
+                        if (!isACEqualEnough(key, actualList, expectedList, actualAlts, expectedAlts)) {
+                            throw makeVariantExceptionFromDifference(key, actualList.toString(), expectedList.toString());
+                        }
+                    }
+                    //we've already gotten rid of stars... I think -- do we have to sort the alts?  Maybe...  I should be using my own AlleleSpecificAnnotationData!!!
+                    final int iterationEnd = ignoreNonRefData && actualAlts.contains(Allele.NON_REF_ALLELE) ? expectedAlts.size()-1 : expectedAlts.size();  //exclusive
+                    for (int i = 0; i < iterationEnd; i++) {
+                        if (i >= actualList.size() || i >= expectedList.size()) {
+                            //TODO: the toStrings here don't do a great job
+                            throw makeVariantExceptionFromDifference(key, actualValue.toString(), expectedValue.toString());
+                        }
+                        if (key.equals(GATKVCFConstants.AS_INBREEDING_COEFFICIENT_KEY)) {
+                            final double actualPerAlleleValue = Double.parseDouble(actualList.get(i).toString());
+                            final double expectedPerAlleleValue = Double.parseDouble(expectedList.get(i).toString());
+                            if (!isAttributeEqualDoubleSmart(key,
+                                    actualPerAlleleValue, expectedPerAlleleValue,
+                                    inbreedingCoeffTolerance)) {
+                                throw makeVariantExceptionFromDifference(key, Double.toString(actualPerAlleleValue), Double.toString(expectedPerAlleleValue));
+                            }
+                        }
+                        if (key.contains("AS_") && key.contains("RankSum")) {
+                            final double actualPerAlleleValue, expectedPerAlleleValue;
+                            if ((!((String) actualList.get(i)).isEmpty() && ((String) actualList.get(i)).equals("NaN"))) {
+                                actualPerAlleleValue = Double.parseDouble(actualList.get(i).toString());
+                                expectedPerAlleleValue = Double.parseDouble(expectedList.get(i).toString());
+                                if (!isAttributeEqualDoubleSmart(key,
+                                        actualPerAlleleValue, expectedPerAlleleValue,
+                                        ranksumTolerance)) {
+                                    throw makeVariantExceptionFromDifference(key, Double.toString(actualPerAlleleValue), Double.toString(expectedPerAlleleValue));
+                                }
+                                continue;
+                            } else {
+                                if (!muteDiffs && !allowNanMismatch) {
+                                    logger.warn("GATK version-specific NaN versus empty AS_RAW annotation discrepancy");
+                                }
+                            }
+                        }
+                        //this needs some cleanup -- two exceptions??
+                       final boolean check;
+                        try
+                       {check = isAttributeValueEqual(key, actualList.get(i), expectedList.get(i)); }
+                       catch (final UserException e){
+                           if (!ignoreStarAttributes && !actualAlts.get(i).equals(Allele.SPAN_DEL) && !actualAlts.get(i).equals(Allele.SPAN_DEL)) {
+                               throw makeVariantExceptionFromDifference(key, actualList.get(i).toString(), expectedList.get(i).toString());
+                           }
+                        }
+                    }
+                } else {  //if not list
+                    try {
+                        if (key.contains("RankSum") && !key.contains("AS_")) {
+                            if (!isAttributeEqualDoubleSmart(key, Double.parseDouble(actualValue.toString()), Double.parseDouble(expectedValue.toString()),
+                                    ranksumTolerance)) {
+                                throw makeVariantExceptionFromDifference(key, actualValue.toString(), actualValue.toString());
+                            }
+                        } else {
+                            isAttributeValueEqual(key, actualValue, expectedValue);
+                        }
+                    } catch (final UserException e) {
+                        if (annotationsThatVaryWithNoCalls.contains(key) && alleleNumberIsDifferent) {
+                            continue;
+                        } else {
+                            if (key.equals(GATKVCFConstants.QUAL_BY_DEPTH_KEY) || key.equals(GATKVCFConstants.AS_QUAL_BY_DEPTH_KEY)) {
+                                final double actualDouble = Double.parseDouble(actualValue.toString());
+                                final double expectedDouble = Double.parseDouble(expectedValue.toString());
+                                final int expectedDP = Integer.parseInt(expected.get(VCFConstants.DEPTH_KEY).toString());
+                                if (qualByDepthDifferenceIsAcceptable(actualDouble, expectedDouble, expectedQual, expectedDP)) {  //QD won't match if DP doesn't
+                                    if (!muteDiffs) {
+                                        logger.warn(key + " difference is within expected tolerances");
+                                    }
+                                    continue;
+                                } else {
+                                    final boolean isDepthEqual;
+                                    try {
+                                        isDepthEqual = isAttributeValueEqual(VCFConstants.DEPTH_KEY, actual.get(VCFConstants.DEPTH_KEY), expected.get(VCFConstants.DEPTH_KEY));
+                                    } catch (final UserException e2) {
+                                        //check expected QD against expected AS_QD because in a few cases actual is wrong
+                                        if (!qualByDepthDifferenceIsAcceptable(Double.parseDouble(actual.get(GATKVCFConstants.QUAL_BY_DEPTH_KEY).toString()),
+                                        Double.parseDouble(actual.get(GATKVCFConstants.AS_QUAL_BY_DEPTH_KEY).toString()), expectedQual, expectedDP)) {
+                                            logger.warn(key + " difference (actual = " + actual.get(key) + " versus expected:"
+                                                    + expected.get(key) + " is larger than expected, but so is DP (actual="
+                                                    + actual.get(VCFConstants.DEPTH_KEY) + " versus expected:" + expected.get(VCFConstants.DEPTH_KEY) + ")");
+                                        }
+                                        continue;
+                                    }
+                                    if (isDepthEqual) {
+                                        throw e;
+                                    }
+                                }
+                            }
+                        }
+                    throw e;
+                    }
+                }
+            }
+            expectedKeys.remove(key);
+        }
+    }
+
+    /**
+     * Generate an exception to throw later
+     * @param thingToCompare    the key to appear in the exception
+     * @param actual
+     * @param expected
+     * @return
+     */
+    private UserException makeVariantExceptionFromDifference(final String thingToCompare, final String actual, final String expected) {
+        return new UserException("Variant contexts have different " + thingToCompare + ": actual has " + actual
+                + " expected has " + expected);
+    }
+
+    /**
+     * Generate an exception to throw later
+     * @param thingToCompare    the key to appear in the exception
+     * @param actual
+     * @param expected
+     * @return
+     */
+    private UserException makeGenotypeExceptionFromDifference(final String thingToCompare, final String actual, final String expected) {
+        return new UserException("Genotypes have different " + thingToCompare + ": actual has " + actual
+                + " expected has " + expected);
+    }
+
+
+    /**
+     *
+     * @param key
+     * @param actual    input VariantContext containing key
+     * @param expected  input VariantContext containing key
+     * @return
+     */
+    private boolean isAttributeValueEqual(final String key, final Object actual, final Object expected) {
+        if (allowNanMismatch && (actual.toString()).equals(".") && expected.toString().equals("NaN")) {
+            return true;
+        }
+        if (!actual.toString().equals(expected.toString())) {
+            throw new UserException("Variant contexts have different attribute values for " + key + ": actual has " + actual.toString()
+                    + " and expected has " + expected.toString());
+        }
+        return actual.toString().equals(expected.toString());
+
+    }
+
+    private boolean isAttributeEqualDoubleSmart(final String key, final double actual, final double expected, final double tolerance) {
+        final double diff = Math.abs(actual - expected);
+        if (diff > tolerance) {
+            throw new UserException("Attribute " + key + " has difference " + String.format("%.3f", diff) + ", which is larger difference than allowed delta " + tolerance);
+        }
+        return true;
+    }
+
+    private void checkGenotypes(final Genotype actual, final Genotype expected) {
+        if (!actual.getSampleName().equals(expected.getSampleName())) {
+            throw new UserException("Sample names do not match");
+        }
+        if (!CollectionUtils.isEqualCollection(actual.getAlleles(), expected.getAlleles())) {
+            throw makeGenotypeExceptionFromDifference("alleles", actual.getAlleles().toString(), expected.getAlleles().toString());
+        }
+
+        if (!ignoreGenotypePhasing) {
+            if (!actual.getGenotypeString(false).equals(expected.getGenotypeString(false))) {
+                throw makeGenotypeExceptionFromDifference("genotype string", actual.getGenotypeString(false), expected.getGenotypeString(false));
+            }
+            if (actual.isPhased() != expected.isPhased()) {
+                throw makeGenotypeExceptionFromDifference("phasing status", Boolean.toString(actual.isPhased()), Boolean.toString(expected.isPhased()));
+            }
+        }
+        if (ignoreHomRefAttributes && actual.isHomRef()) {
+            return;
+        }
+        if (actual.hasDP() != expected.hasDP()) {
+            throw makeGenotypeExceptionFromDifference("DP presence", Boolean.toString(actual.hasDP()), Boolean.toString(expected.hasDP()));
+        }
+        if (actual.hasAD() != expected.hasAD()) {
+            throw makeGenotypeExceptionFromDifference("AD presence", Boolean.toString(actual.hasAD()), Boolean.toString(expected.hasAD()));
+        }
+        if (actual.hasGQ() != expected.hasGQ()) {
+            throw makeGenotypeExceptionFromDifference("GQ presence", Boolean.toString(actual.hasGQ()), Boolean.toString(expected.hasGQ()));
+        }
+        if (!actual.isHomRef()) {
+            if (actual.hasGQ() && (Math.abs(actual.getGQ() - expected.getGQ())) > likelihoodTolerance) {
+                //allele subsetting can return GQs over 99, which apparently are capped on VCF write
+                if (actual.getGQ() < 99 || expected.getGQ() < 99) {
+                    throw makeGenotypeExceptionFromDifference("GQ value", Integer.toString(actual.getGQ()), Integer.toString(expected.getGQ()));
+                }
+            }
+        }
+        if (ignoreGenotypeAnnotations) {
+            return;
+        }
+        //allow DP difference due to non-ref AD correction
+        if (actual.hasDP() && expected.hasDP()) {
+            if (actual.getDP() != expected.getDP()) {
+                if (dpChange == 0 && expected.getDP() - actual.getDP() != expected.getAD()[expected.getAD().length - 1]) {
+                    throw makeGenotypeExceptionFromDifference("DP value", Integer.toString(actual.getDP()), Integer.toString(expected.getDP()));
+                }
+                if (actual.getDP() - expected.getDP() > dpChange) {
+                    throw new UserException("DP difference exceeds allowable tolerance of " + dpChange
+                            + ", actual has " + Integer.toString(actual.getDP()) + " expected has " + Integer.toString(expected.getDP()));
+                }
+                if (actual.hasAD() && (!Arrays.equals(actual.getAD(), expected.getAD()))) {
+                    if (dpChange == 0 && actual.getAD()[actual.getAD().length - 1] == expected.getAD()[expected.getAD().length - 1]) {  //non-ref differences are okay, but if there's an AD different that's not non-ref we're in trouble
+                        throw makeGenotypeExceptionFromDifference("AD values", Arrays.toString(actual.getAD()), Arrays.toString(expected.getAD()));
+                    }
+                    for (int i = 0; i < actual.getAD().length - 1; i++) {
+                        if (actual.getAD()[i] - expected.getAD()[i] > dpChange) {
+                            throw new UserException("AD difference exceeds allowable tolerance of " + dpChange
+                                    + ", actual has " + actual.getAD().toString() + " expected has " + expected.getAD().toString());
+                        }
+                    }
+                }
+            }
+
+            if (actual.hasPL() != expected.hasPL()) {
+                throw makeGenotypeExceptionFromDifference("PL presence", Boolean.toString(actual.hasPL()), Boolean.toString(expected.hasPL()));
+            }
+            if (actual.hasPL() && expected.hasPL()) {
+                final int[] actualPls = actual.getPL();
+                final int[] expectedPls = expected.getPL();
+                if (actualPls.length != expectedPls.length) {
+                    throw new UserException("PL lengths for genotype vary: actual is size " + actualPls.length + " and expected is " + expectedPls.length);
+                }
+                for (int i = 0; i < actualPls.length; i++) {
+                    if (Math.abs(actualPls[i] - expectedPls[i]) > likelihoodTolerance) {
+                        throw makeGenotypeExceptionFromDifference("PL value", Arrays.toString(actual.getPL()), Arrays.toString(expected.getPL()));
+                    }
+                }
+            }
+        }
+    }
+
+    private void throwOrWarn(final UserException e) {
+        if (muteDiffs && (alleleNumberIsDifferent || inbreedingCoeffIsDifferent)) {
+            return;
+        }
+        if (warnOnError || finishBeforeFailing) {
+            if (warningsOutput != null) {
+                outputStream.println(e.getMessage());
+            }
+            logger.warn("***** " + e.getMessage() + " *****");
+            if (finishBeforeFailing) {
+                failOnCompletion = true;
+            }
+        } else {
+            throw e;
+        }
+    }
+
+    //Non-reblocked GVCFs can have alleles that aren't called, so trim them
+    private VariantContext trimAlleles(final VariantContext variant, final List<VariantContext> overlappingDels) {
+        final Allele ref = variant.getReference();
+        final Set<Allele> relevantAlleles = new LinkedHashSet<>();
+        for (final Genotype g : variant.getGenotypes()) {
+            final List<Allele> gtAlleles = g.getAlleles();
+            relevantAlleles.add(ref);
+            if (!gtAlleles.contains(Allele.NO_CALL)) {  //in theory there could be half no-calls, but I've never seen one
+                if (overlappingDels.size() > 0) {
+                    relevantAlleles.addAll(gtAlleles);
+                } else relevantAlleles.addAll(gtAlleles.stream().filter(GATKVariantContextUtils::isConcreteAlt).collect(Collectors.toList()));
+            }
+        }
+        final VariantContextBuilder vcBuilder = new VariantContextBuilder(variant);
+        final List<Allele> orderedRelevantAlleles = new ArrayList<>(relevantAlleles);
+        if (vcBuilder.getGenotypes().size() == 1 && !ignoreNonRefData) {
+            orderedRelevantAlleles.add(Allele.NON_REF_ALLELE);
+        }
+        vcBuilder.alleles(orderedRelevantAlleles);
+
+        //NOTE that we use BEST_MATCH_TO_ORIGINAL for post-reblocked VCFs with no hom ref PLs
+        final GenotypesContext gc = AlleleSubsettingUtils.subsetAlleles(variant.getGenotypes(), defaultPloidy,
+                variant.getAlleles(), orderedRelevantAlleles, null, GenotypeAssignmentMethod.BEST_MATCH_TO_ORIGINAL);
+        vcBuilder.genotypes(gc);
+
+        final Map<String,Object> subsetAnnotations = ReblockGVCF.subsetAnnotationsIfNecessary(annotatorEngine, false, VCFConstants.GENOTYPE_POSTERIORS_KEY, variant, vcBuilder.make(), annotationsToKeep);
+
+        return variant.getGenotype(0).isHomRef() ? vcBuilder.make() : GATKVariantContextUtils.reverseTrimAlleles(vcBuilder.attributes(subsetAnnotations).make());
+    }
+
+    /*
+     * Some code paths expect significant differences, so focusing on high quality variants is useful.
+     */
+    private boolean isHighQuality(final VariantContext vc) {
+        if (vc.getGenotypes().size() == 1) {
+            //genotyping engine returns 0.01 for hom-ref SNPs, probably because of prior
+            final Genotype genotype = vc.getGenotype(0);
+            if (!genotype.hasPL()) {
+                return false;
+            }
+            if (genotype.isHomRef()) {
+                return false;
+            }
+            if (genotype.getPL()[0] == 0) {
+                return false;
+            }
+            if (genotype.getAlleles().contains(Allele.NON_REF_ALLELE)) {
+                return false;
+            }
+            return vc.getPhredScaledQual() > 0.01 && (MathUtils.arrayMax(genotype.getPL()) > 0);
+        } else {
+            for (final Genotype genotype : vc.getGenotypes()) {
+                if (genotype.isHomRef()) {
+                    continue;
+                }
+                if (passesGnomadAdjCriteria(genotype)) {
+                    return true;
+                }
+            }
+            return false;
+        }
+    }
+
+    /*
+     * This is for known significant changes so we can compare only high quality genotypes as defined by these gnomAD adj criteria.
+     * https://gnomad.broadinstitute.org/news/2020-10-gnomad-v3-1-new-content-methods-annotations-and-data-availability/
+     */
+    private boolean passesGnomadAdjCriteria(final Genotype g) {
+        if (!g.hasGQ() || g.getGQ() < 20) {
+            return false;
+        }
+        if (!g.hasDP() || g.getDP() < 10) {
+            return false;
+        }
+        if (g.isHet()) {
+            if (!g.hasAD()) {
+                return false;
+            }
+            final int[] ad = g.getAD();
+            final double alleleBalance;
+            if (g.isHetNonRef()) {
+                alleleBalance = ad[2] / ((double) ad[1] + ad[2]);
+
+            } else {
+                alleleBalance = ad[1] / ((double) ad[0] + ad[1]);
+            }
+            if (alleleBalance >= 0.2 && alleleBalance <= 0.8) {
+                return true;
+            }
+        }
+        return false;
+    }
+
+    private boolean isACEqualEnough(final String key, final List<? extends Object> actualList, final List<? extends Object> expectedList,
+                                    final List<Allele> actualAlts, final List<Allele> expectedAlts) {
+        if (actualList.size() != expectedList.size()) {
+            return false;
+        }
+        //trimming may drop AC=0 alts, but GATK convention is to put them last, so that shouldn't be an issue
+        for (int i = 0; i < actualAlts.size(); i++) {
+            if (actualAlts.get(i).equals(Allele.SPAN_DEL)) {
+                continue;
+            }
+            if (actualAlts.get(i).equals(expectedAlts.get(i))) {
+                final int expectedValue = Integer.parseInt(expectedList.get(i).toString());
+                final int actualValue = Integer.parseInt(actualList.get(i).toString());
+                //TODO: and....?
+            } else {
+                throwOrWarn(new UserException("Alleles are not ordered the same"));
+                return false;
+            }
+        }
+        return true;
+    }
+
+    private boolean qualByDepthWillHaveJitter(final double expectedQual, final int expectedDepth) {
+        final double qdEstimate = expectedQual / (double) expectedDepth;
+        if (QualByDepth.fixTooHighQD(qdEstimate) != qdEstimate || qdEstimate > 34.9) {  //I don't know why we get different values at 34.9 -- there must be rounding somewhere?
+            return true;
+        }
+        return false;
+    }
+
+    private boolean qualByDepthDifferenceIsAcceptable(final double actual, final double expected, final double expectedQual, final int expectedDP) {
+        final double diff = Math.abs(expected - actual);
+        final double relativeDiff = diff / (expected);
+        return expected > 25.0 || relativeDiff < 0.01 || diff < 0.5 ////25 is in the "jitter" zone
+                || qualByDepthWillHaveJitter(expectedQual, expectedDP);
+    }
+
+    public Object onTraversalSuccess() {
+        if (failOnCompletion) {
+            throw new UserException("Some comparisons failed.  See stderr log for details.");
+        }
+        return null;
+    }
+
+    @Override
+    public void closeTool() {
+        if ( outputStream != null ) {
+            outputStream.close();
+        }
+    }
+}
diff --git a/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVariantContextUtils.java b/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVariantContextUtils.java
index 5451aef6f54..61d5306069c 100644
--- a/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVariantContextUtils.java
+++ b/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVariantContextUtils.java
@@ -740,6 +740,19 @@ public static boolean containsInlineIndel(final Allele ref, final Collection<All
         return false;
     }
 
+    /**
+     * Is there a real ALT allele that's not <NON_REF> or * ?
+     * @param alleles   alleles in the called genotype
+     * @return true if the genotype has a called allele that is a "real" alternate
+     */
+    public static boolean genotypeHasConcreteAlt(final List<Allele> alleles) {
+        return alleles.stream().anyMatch(GATKVariantContextUtils::isConcreteAlt);
+    }
+
+    public static boolean isConcreteAlt(final Allele a) {
+        return !a.isReference() && !a.isSymbolic() && !a.equals(Allele.SPAN_DEL);
+    }
+
     public enum GenotypeMergeType {
         /**
          * Make all sample genotypes unique by file. Each sample shared across RODs gets named sample.ROD.
diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/VCFComparatorIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/VCFComparatorIntegrationTest.java
new file mode 100644
index 00000000000..e60bf275a8d
--- /dev/null
+++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/VCFComparatorIntegrationTest.java
@@ -0,0 +1,116 @@
+package org.broadinstitute.hellbender.tools.walkers.variantutils;
+
+import org.broadinstitute.hellbender.CommandLineProgramTest;
+import org.broadinstitute.hellbender.exceptions.UserException;
+import org.testng.Assert;
+import org.testng.annotations.DataProvider;
+import org.broadinstitute.hellbender.testutils.ArgumentsBuilder;
+import org.broadinstitute.hellbender.testutils.IntegrationTestSpec;
+import org.testng.annotations.Test;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.Arrays;
+
+public class VCFComparatorIntegrationTest extends CommandLineProgramTest {
+
+    private static final String TEST_DATA_DIRECTORY = publicTestDir + "org/broadinstitute/hellbender/tools/walkers/VCFComparator/";
+    private static final String TEST_OUTPUT_DIRECTORY = TEST_DATA_DIRECTORY + "/expected/";
+    private static final String DEFAULT_WARP_SETTINGS = "--ignore-attribute VQSLOD --ignore-attribute AS_VQSLOD --ignore-filters --ignore-attribute culprit  --ignore-attribute AS_culprit --ignore-attribute AS_FilterStatus --ignore-attribute ExcessHet --ignore-attribute AS_SOR --ignore-attribute AS_FS --ignore-attribute AS_BaseQRankSum --ignore-attribute AS_ReadPosRankSum --ignore-attribute AS_MQRankSum";
+
+    @DataProvider(name = "getTestVcfs")
+    public Object[][] getTestVcfs() {
+        return new Object[][] {
+                { " -L chr1:186475", "expected_warning_as_vqslod.txt" },
+                { " -L chr1:186475 --ignore-attribute AS_VQSLOD", "empty_file.txt" },
+                { " -L chr1:187471 --ignore-attribute AS_VQSLOD", "expected_warning_filter.txt" },
+                { " -L chr1:186475-945669 " + DEFAULT_WARP_SETTINGS, "empty_file.txt" },
+                { " -L chr1:945670 " + DEFAULT_WARP_SETTINGS, "qual_diff_warning.txt"}, // different QUAL values
+                { " -L chr1:945670 --qual-change-allowed 0.1 --ignore-attribute AS_VQSLOD", "empty_file.txt"},
+                { " -L chr1:186475 --mute-acceptable-diffs", "empty_file.txt" } // low quality site is muted even though the AS_VQSLOD is different
+        };
+    }
+
+    @Test(dataProvider = "getTestVcfs")
+    public void testAnnotationDifferences(String args, String expectedWarnings) throws IOException {
+        final IntegrationTestSpec testSpec = new IntegrationTestSpec(
+                        " -R " + hg38Reference +
+                        " -V:actual " + TEST_DATA_DIRECTORY + "actual.vcf" +
+                        " -V:expected " + TEST_DATA_DIRECTORY + "expected.vcf" +
+                        " --output-warnings %s" +
+                        " --warn-on-errors" +
+                        args,
+                Arrays.asList(TEST_OUTPUT_DIRECTORY + expectedWarnings)
+        );
+        testSpec.executeTest("testVcfs", this);
+    }
+
+    @Test
+    public void testExpectedFailure() {
+        final File actual = new File(TEST_DATA_DIRECTORY + "actual.vcf");
+        final File expected = new File(TEST_DATA_DIRECTORY + "expected.vcf");
+        final ArgumentsBuilder args = new ArgumentsBuilder();
+        args.addReference(hg38Reference);
+        args.add("V:actual", actual);
+        args.add("V:expected", expected);
+        args.addInterval("chr1:186475");
+        args.add("warn-on-errors", true);
+
+        //warn on errors alone shouldn't fail
+        runCommandLine(args);
+
+        //adding finish-before-failing should fail
+        args.add("finish-before-failing", true);
+        Assert.assertThrows(UserException.class, () -> runCommandLine(args));
+    }
+
+    @DataProvider(name = "getTestGvcfs")
+    public Object[][] getTestGvcfs() {
+        return new Object[][] {
+                { " -L chr1:864084-864610", "empty_file.txt" }, //matching ref blocks
+                { " -L chr1:54682-347969", "ref_block_warning.txt"}, // non-matching ref block
+                { " -L chr1:792417", "tree_score_warning.txt"}, // variant site
+                { " -L chr1:792417 --ignore-non-ref-data --" +
+                        ReblockGVCF.ANNOTATIONS_TO_KEEP_LONG_NAME + " TREE_SCORE", "tree_score_warning.txt"}, // when non-ref data is dropped non-GATK annotations can be dropped
+                { " -L chr1:792417 --ignore-attribute TREE_SCORE", "empty_file.txt"}
+        };
+    }
+
+    @Test(dataProvider = "getTestGvcfs")
+    public void testGvcfs(String args, String expectedWarnings) throws IOException {
+        final IntegrationTestSpec testSpec = new IntegrationTestSpec(
+                " -R " + hg38Reference +
+                        " -V:actual " + TEST_DATA_DIRECTORY + "actual.NA12878.rb.g.vcf" +
+                        " -V:expected " + TEST_DATA_DIRECTORY + "expected.NA12878.rb.g.vcf" +
+                        " --output-warnings %s" +
+                        " --warn-on-errors" +
+                        args,
+                Arrays.asList(TEST_OUTPUT_DIRECTORY + expectedWarnings));
+        testSpec.executeTest("testGvcfs", this);
+    }
+
+    @Test
+    public void testMixedPloidy() throws IOException {
+        final IntegrationTestSpec expectDiploid = new IntegrationTestSpec(
+                " -R " + hg38Reference +
+                        " -L chrX:66780645" +
+                        " -V:actual " + TEST_DATA_DIRECTORY + "haploid.rb.g.vcf" +
+                        " -V:expected " + TEST_DATA_DIRECTORY + "diploid.rb.g.vcf" +
+                        " --output-warnings %s" +
+                        " --warn-on-errors",
+                Arrays.asList(TEST_OUTPUT_DIRECTORY + "haploid_warning.txt"));
+        expectDiploid.executeTest("testMixedPloidy", this);
+
+        // check the other way as far as which ploidy is expected vs actual
+        final IntegrationTestSpec expectHaploid = new IntegrationTestSpec(
+                " -R " + hg38Reference +
+                        " -L chrX:66780645" +
+                        " -V:actual " + TEST_DATA_DIRECTORY + "diploid.rb.g.vcf" +
+                        " -V:expected " + TEST_DATA_DIRECTORY + "haploid.rb.g.vcf" +
+                        " --output-warnings %s" +
+                        " --warn-on-errors",
+                Arrays.asList(TEST_OUTPUT_DIRECTORY + "haploid_warning2.txt"));
+        expectHaploid.executeTest("testMixedPloidy", this);
+    }
+
+}
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/actual.NA12878.rb.g.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/actual.NA12878.rb.g.vcf
new file mode 100644
index 00000000000..6c6c67d48fb
--- /dev/null
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/actual.NA12878.rb.g.vcf
@@ -0,0 +1,3509 @@
+##fileformat=VCFv4.2
+##ALT=<ID=NON_REF,Description="Represents any possible alternative allele not already represented at this location by REF and ALT">
+##FILTER=<ID=LowQual,Description="Low quality">
+##FILTER=<ID=PASS,Description="All filters passed">
+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
+##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another; will always be heterozygous and is not intended to describe called alleles">
+##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)">
+##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
+##GATKCommandLine=<ID=HaplotypeCaller,CommandLine="HaplotypeCaller --gvcf-gq-bands 10 --gvcf-gq-bands 20 --gvcf-gq-bands 30 --gvcf-gq-bands 40 --gvcf-gq-bands 50 --gvcf-gq-bands 60 --gvcf-gq-bands 70 --gvcf-gq-bands 80 --gvcf-gq-bands 90 --flow-mode ADVANCED --bam-writer-type CALLED_HAPLOTYPES_NO_READS --smith-waterman FASTEST_AVAILABLE --emit-ref-confidence GVCF --output downsampled_NA12878.g.vcf.gz --intervals /cromwell_root/broad-gotc-dev-cromwell-execution/TestBroadInternalUltimaGenomics/c8c1c028-6ffa-4fda-a93b-06a19b57ae78/call-BroadInternalUltimaGenomics/BroadInternalUltimaGenomics/ba495953-a521-466f-8443-61169b1f8a52/call-UltimaGenomicsWholeGenomeGermline/UltimaGenomicsWholeGenomeGermline/82255504-500c-46e9-9062-2a80811f1213/call-ScatterIntervalList/cacheCopy/glob-cb4648beeaff920acb03de7603c06f98/199scattered.interval_list --input gs://broad-gotc-dev-cromwell-execution/TestBroadInternalUltimaGenomics/c8c1c028-6ffa-4fda-a93b-06a19b57ae78/call-BroadInternalUltimaGenomics/BroadInternalUltimaGenomics/ba495953-a521-466f-8443-61169b1f8a52/call-UltimaGenomicsWholeGenomeGermline/UltimaGenomicsWholeGenomeGermline/82255504-500c-46e9-9062-2a80811f1213/call-UltimaGenomicsWholeGenomeCramOnly/UltimaGenomicsWholeGenomeCramOnly/9e4467ae-fc2b-4b33-aec0-f8aff47417cd/call-AlignmentAndMarkDuplicates/AlignmentAndMarkDuplicates/22485d8b-69d6-4f7c-a83e-b4b130678b6f/call-MarkDuplicatesSpark/downsampled_NA12878.aligned.sorted.duplicates_marked.bam --read-index /cromwell_root/broad-gotc-dev-cromwell-execution/TestBroadInternalUltimaGenomics/c8c1c028-6ffa-4fda-a93b-06a19b57ae78/call-BroadInternalUltimaGenomics/BroadInternalUltimaGenomics/ba495953-a521-466f-8443-61169b1f8a52/call-UltimaGenomicsWholeGenomeGermline/UltimaGenomicsWholeGenomeGermline/82255504-500c-46e9-9062-2a80811f1213/call-UltimaGenomicsWholeGenomeCramOnly/UltimaGenomicsWholeGenomeCramOnly/9e4467ae-fc2b-4b33-aec0-f8aff47417cd/call-AlignmentAndMarkDuplicates/AlignmentAndMarkDuplicates/22485d8b-69d6-4f7c-a83e-b4b130678b6f/call-MarkDuplicatesSpark/downsampled_NA12878.aligned.sorted.duplicates_marked.bam.bai --reference /cromwell_root/gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta --annotation AssemblyComplexity --annotation-group StandardAnnotation --annotation-group StandardHCAnnotation --annotation-group AS_StandardAnnotation --assembly-complexity-reference-mode true --use-posteriors-to-calculate-qual false --dont-use-dragstr-priors false --use-new-qual-calculator true --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --genotype-assignment-method USE_PLS_TO_ASSIGN --contamination-fraction-to-filter 0.0 --output-mode EMIT_VARIANTS_ONLY --all-site-pls false --flow-likelihood-parallel-threads 0 --flow-likelihood-optimized-comp false --trim-to-haplotype true --exact-matching false --flow-use-t0-tag false --flow-remove-non-single-base-pair-indels false --flow-remove-one-zero-probs false --flow-quantization-bins 121 --flow-fill-empty-bins-value 0.001 --flow-symmetric-indel-probs false --flow-report-insertion-or-deletion false --flow-disallow-probs-larger-than-call false --flow-lump-probs false --flow-retain-max-n-probs-base-format false --flow-probability-scaling-factor 10 --flow-order-cycle-length 4 --keep-boundary-flows false --floor-blocks false --indel-size-to-eliminate-in-ref-model 10 --disable-optimizations false --dragen-mode false --dragen-378-concordance-mode false --apply-bqd false --apply-frd false --disable-spanning-event-genotyping false --transform-dragen-mapping-quality false --mapping-quality-threshold-for-genotyping 20 --max-effective-depth-adjustment-for-frd 0 --just-determine-active-regions false --dont-genotype false --do-not-run-physical-phasing false --do-not-correct-overlapping-quality false --use-filtered-reads-for-annotations false --use-flow-aligner-for-stepwise-hc-filtering false --adaptive-pruning false --do-not-recover-dangling-branches false --recover-dangling-heads false --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --pruning-seeding-lod-threshold 9.210340371976184 --max-unpruned-variants 100 --linked-de-bruijn-graph false --disable-artificial-haplotype-recovery false --enable-legacy-graph-cycle-detection false --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --num-matching-bases-in-dangling-end-to-recover -1 --error-correction-log-odds -Infinity --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --dragstr-het-hom-ratio 2 --dont-use-dragstr-pair-hmm-scores false --pair-hmm-gap-continuation-penalty 10 --expected-mismatch-rate-for-read-disqualification 0.02 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --disable-symmetric-hmm-normalizing false --disable-cap-base-qualities-to-map-quality false --enable-dynamic-read-disqualification-for-genotyping false --dynamic-read-disqualification-threshold 1.0 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --flow-hmm-engine-min-indel-adjust 6 --flow-hmm-engine-flat-insertion-penatly 45 --flow-hmm-engine-flat-deletion-penatly 45 --pileup-detection false --use-pdhmm false --use-pdhmm-overlap-optimization false --make-determined-haps-from-pd-code false --print-pileupcalling-status false --fallback-gga-if-pdhmm-fails true --pileup-detection-enable-indel-pileup-calling false --pileup-detection-active-region-phred-threshold 0.0 --num-artificial-haplotypes-to-add-per-allele 5 --artifical-haplotype-filtering-kmer-size 10 --pileup-detection-snp-alt-threshold 0.1 --pileup-detection-indel-alt-threshold 0.1 --pileup-detection-absolute-alt-depth 0.0 --pileup-detection-snp-adjacent-to-assembled-indel-range 5 --pileup-detection-snp-basequality-filter 12 --pileup-detection-bad-read-tolerance 0.0 --pileup-detection-proper-pair-read-badness true --pileup-detection-edit-distance-read-badness-threshold 0.08 --pileup-detection-chimeric-read-badness true --pileup-detection-template-mean-badness-threshold 0.0 --pileup-detection-template-std-badness-threshold 0.0 --pileup-detection-filter-assembly-alt-bad-read-tolerance 0.0 --pileup-detection-edit-distance-read-badness-for-assembly-filtering-threshold 0.12 --dont-use-soft-clipped-bases false --override-fragment-softclip-check false --min-base-quality-score 10 --max-mnp-distance 0 --force-call-filtered-alleles false --reference-model-deletion-quality 30 --soft-clip-low-quality-ends false --allele-informative-reads-overlap-margin 2 --smith-waterman-dangling-end-match-value 25 --smith-waterman-dangling-end-mismatch-penalty -50 --smith-waterman-dangling-end-gap-open-penalty -110 --smith-waterman-dangling-end-gap-extend-penalty -6 --smith-waterman-haplotype-to-reference-match-value 200 --smith-waterman-haplotype-to-reference-mismatch-penalty -150 --smith-waterman-haplotype-to-reference-gap-open-penalty -260 --smith-waterman-haplotype-to-reference-gap-extend-penalty -11 --smith-waterman-read-to-haplotype-match-value 10 --smith-waterman-read-to-haplotype-mismatch-penalty -15 --smith-waterman-read-to-haplotype-gap-open-penalty -30 --smith-waterman-read-to-haplotype-gap-extend-penalty -5 --flow-assembly-collapse-hmer-size 0 --flow-assembly-collapse-partial-mode false --flow-filter-alleles false --flow-filter-alleles-qual-threshold 30.0 --flow-filter-alleles-sor-threshold 3.0 --flow-filter-lone-alleles false --flow-filter-alleles-debug-graphs false --min-assembly-region-size 50 --max-assembly-region-size 300 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --assembly-region-padding 100 --padding-around-indels 75 --padding-around-snps 20 --padding-around-strs 75 --max-extension-into-assembly-region-padding-legacy 25 --max-reads-per-alignment-start 50 --enable-legacy-assembly-region-trimming false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false --allow-old-rms-mapping-quality-annotation-data false",Version="4.6.0.0",Date="July 1, 2024 at 5:24:13 PM GMT">
+##GATKCommandLine=<ID=SelectVariants,CommandLine="SelectVariants --output actual.NA12878.rb.g.vcf --variant gs://broad-gotc-test-results/dev/UltimaGenomicsWholeGenomeGermline/plumbing/2024-07-19-21-10-44/NA12878.downsampled/downsampled_NA12878.annotated.rb.g.vcf.gz --intervals chr1:186475-945670 --apply-jexl-filters-first false --invertSelect false --exclude-non-variants false --exclude-filtered false --preserve-alleles false --remove-unused-alternates false --restrict-alleles-to ALL --keep-original-ac false --keep-original-dp false --mendelian-violation false --invert-mendelian-violation false --mendelian-violation-qual-threshold 0.0 --select-random-fraction 1.0 --remove-fraction-genotypes 0.0 --ignore-non-ref-in-types false --fully-decode false --max-indel-size 2147483647 --min-indel-size 0 --max-filtered-genotypes 2147483647 --min-filtered-genotypes 0 --max-fraction-filtered-genotypes 1.0 --min-fraction-filtered-genotypes 0.0 --max-nocall-number 2147483647 --max-nocall-fraction 1.0 --set-filtered-gt-to-nocall false --allow-nonoverlapping-command-line-samples false --suppress-reference-path false --fail-on-unsorted-genotype false --genomicsdb-max-alternate-alleles 50 --call-genotypes false --genomicsdb-use-bcf-codec false --genomicsdb-shared-posixfs-optimizations false --genomicsdb-use-gcs-hdfs-connector false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false",Version="4.6.0.0-19-g6a6872f-SNAPSHOT",Date="August 2, 2024 at 9:11:07 AM EDT">
+##GVCFBlock0-20=minGQ=0(inclusive),maxGQ=20(exclusive)
+##GVCFBlock20-30=minGQ=20(inclusive),maxGQ=30(exclusive)
+##GVCFBlock30-40=minGQ=30(inclusive),maxGQ=40(exclusive)
+##GVCFBlock40-100=minGQ=40(inclusive),maxGQ=100(exclusive)
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
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+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
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+##INFO=<ID=AS_SOR,Number=A,Type=Float,Description="Allele specific strand Odds Ratio of 2x|Alts| contingency table to detect allele specific strand bias">
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+##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
+##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
+##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
+##INFO=<ID=FILTERED_HAPS,Number=1,Type=Integer,Description="Haplotypes filtered out by the haplotype filtering code">
+##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
+##INFO=<ID=HAPCOMP,Number=A,Type=Integer,Description="Edit distances of each alt allele's most common supporting haplotype from closest germline haplotype, excluding differences at the site in question.">
+##INFO=<ID=HAPDOM,Number=A,Type=Float,Description="For each alt allele, fraction of read support that best fits the most-supported haplotype containing the allele">
+##INFO=<ID=HEC,Number=.,Type=Integer,Description="Counts of support for haplotype groups excluding difference at the site in question.">
+##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
+##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
+##INFO=<ID=MQ_DP,Number=1,Type=Integer,Description="Depth over variant samples for better MQ calculation (deprecated -- use RAW_MQandDP instead.)">
+##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
+##INFO=<ID=QUALapprox,Number=1,Type=Integer,Description="Sum of PL[0] values; used to approximate the QUAL score">
+##INFO=<ID=RAW_GT_COUNT,Number=3,Type=Integer,Description="Counts of genotypes w.r.t. the reference allele in the following order: 0/0, 0/*, */*, i.e. all alts lumped together; for use in calculating excess heterozygosity">
+##INFO=<ID=RAW_MQandDP,Number=2,Type=Integer,Description="Raw data (sum of squared MQ and total depth) for improved RMS Mapping Quality calculation. Incompatible with deprecated RAW_MQ formulation.">
+##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
+##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
+##INFO=<ID=SUSP_NOISY_ADJACENT_TP_VARIANT,Number=0,Type=Flag,Description="Indicates a locus where false positive allele might be affecting a true positive allele">
+##INFO=<ID=TREE_SCORE,Number=1,Type=Float,Description="Filtering score">
+##INFO=<ID=VarDP,Number=1,Type=Integer,Description="(informative) depth over variant genotypes">
+##INFO=<ID=XC,Number=1,Type=Integer,Description="Indicates longer hmer collapsing took place (this is a flow-based specific tag)">
+##bcftools_annotateCommand=annotate -a /cromwell_root/broad-gotc-dev-cromwell-execution/TestUltimaGenomicsWholeGenomeGermline/95686f11-60d8-47f2-8dd5-daaa98b55731/call-UltimaGenomicsWholeGenomeGermline/UltimaGenomicsWholeGenomeGermline/cb6fc7d2-4bb3-4241-a6dc-89bc2ed6c696/call-FilterVCF/downsampled_NA12878.filtered.vcf.gz -c TREE_SCORE -o downsampled_NA12878.annotated.g.vcf.gz -O z /cromwell_root/broad-gotc-dev-cromwell-execution/TestUltimaGenomicsWholeGenomeGermline/95686f11-60d8-47f2-8dd5-daaa98b55731/call-UltimaGenomicsWholeGenomeGermline/UltimaGenomicsWholeGenomeGermline/cb6fc7d2-4bb3-4241-a6dc-89bc2ed6c696/call-MergeVCFs/cacheCopy/downsampled_NA12878.g.vcf.gz; Date=Mon Jul  1 20:44:39 2024
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+##source=HaplotypeCaller
+##source=SelectVariants
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG03476
+chr1	54682	.	C	<NON_REF>	.	.	END=207666	GT:DP:GQ	0/0:5:0
+chr1	257667	.	G	<NON_REF>	.	.	END=297968	GT:DP:GQ	0/0:0:0
+chr1	347969	.	G	<NON_REF>	.	.	END=535988	GT:DP:GQ	0/0:0:0
+chr1	585989	.	G	<NON_REF>	.	.	END=792416	GT:DP:GQ	0/0:0:0
+chr1	792417	.	C	CA,<NON_REF>	30.44	.	ASSEMBLED_HAPS=4;AS_QUALapprox=|40|0;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|4.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|0,0|0,0;AS_VarDP=0|0|0;DP=1;FILTERED_HAPS=0;QUALapprox=40;RAW_GT_COUNT=0,0,1;RAW_MQandDP=4,1;TREE_SCORE=0.311083;VarDP=1	GT:AD:DP:GQ:PGT:PID:PL:PS:SB	1|1:0,1,0:1:3:0|1:792417_C_CA:40,3,0,45,3,40:792417:0,0,1,0
+chr1	792418	.	T	<NON_REF>	.	.	END=792434	GT:DP:GQ	0/0:1:0
+chr1	792435	.	T	C,<NON_REF>	30.48	.	ASSEMBLED_HAPS=4;AS_QUALapprox=|40|0;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|4.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|0,0|0,0;AS_VarDP=0|0|0;DP=1;FILTERED_HAPS=0;QUALapprox=40;RAW_GT_COUNT=0,0,1;RAW_MQandDP=4,1;TREE_SCORE=0.898068;VarDP=1	GT:AD:DP:GQ:PGT:PID:PL:PS:SB	1|1:0,1,0:1:3:0|1:792417_C_CA:40,3,0,45,3,40:792417:0,0,1,0
+chr1	792436	.	C	<NON_REF>	.	.	END=792472	GT:DP:GQ	0/0:1:0
+chr1	792473	.	C	T,<NON_REF>	30.48	.	ASSEMBLED_HAPS=4;AS_QUALapprox=|40|0;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|4.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|0,0|0,0;AS_VarDP=0|0|0;DP=1;FILTERED_HAPS=0;QUALapprox=40;RAW_GT_COUNT=0,0,1;RAW_MQandDP=4,1;TREE_SCORE=0.869101;VarDP=1	GT:AD:DP:GQ:PGT:PID:PL:PS:SB	1|1:0,1,0:1:3:0|1:792473_C_T:40,3,0,45,3,40:792473:0,0,1,0
+chr1	792474	.	G	<NON_REF>	.	.	END=792490	GT:DP:GQ	0/0:1:0
+chr1	792491	.	G	GA,<NON_REF>	30.44	.	ASSEMBLED_HAPS=4;AS_QUALapprox=|40|0;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|4.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|0,0|0,0;AS_VarDP=0|0|0;DP=1;FILTERED_HAPS=0;QUALapprox=40;RAW_GT_COUNT=0,0,1;RAW_MQandDP=4,1;TREE_SCORE=0.336054;VarDP=1	GT:AD:DP:GQ:PGT:PID:PL:PS:SB	1|1:0,1,0:1:3:0|1:792473_C_T:40,3,0,45,3,40:792473:0,0,1,0
+chr1	792492	.	T	<NON_REF>	.	.	END=792509	GT:DP:GQ	0/0:1:0
+chr1	792510	.	T	C,<NON_REF>	30.48	.	ASSEMBLED_HAPS=4;AS_QUALapprox=|40|0;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|4.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|0,0|0,0;AS_VarDP=0|0|0;DP=1;FILTERED_HAPS=0;QUALapprox=40;RAW_GT_COUNT=0,0,1;RAW_MQandDP=4,1;TREE_SCORE=0.838672;VarDP=1	GT:AD:DP:GQ:PGT:PID:PL:PS:SB	1|1:0,1,0:1:3:0|1:792473_C_T:40,3,0,45,3,40:792473:0,0,1,0
+chr1	792511	.	C	<NON_REF>	.	.	END=792532	GT:DP:GQ	0/0:1:0
+chr1	792533	.	A	G,<NON_REF>	30.48	.	ASSEMBLED_HAPS=4;AS_QUALapprox=|40|0;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|4.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|0,0|0,0;AS_VarDP=0|0|0;DP=1;FILTERED_HAPS=0;QUALapprox=40;RAW_GT_COUNT=0,0,1;RAW_MQandDP=4,1;TREE_SCORE=0.836882;VarDP=1	GT:AD:DP:GQ:PGT:PID:PL:PS:SB	1|1:0,1,0:1:3:0|1:792473_C_T:40,3,0,45,3,40:792473:0,0,1,0
+chr1	792534	.	C	<NON_REF>	.	.	END=853826	GT:DP:GQ	0/0:4:0
+chr1	853827	.	CGCCGTGTGGTAAACTGATGAACCCCGACCCTGATCAACATGAGATGACT	C,<NON_REF>	65.60	.	ASSEMBLED_HAPS=2;AS_QUALapprox=|73|0;AS_RAW_BaseQRankSum=|0.9,1|NaN;AS_RAW_MQ=3600.00|4292.00|0.00;AS_RAW_MQRankSum=|-1.0,1|NaN;AS_RAW_ReadPosRankSum=|0.0,1|NaN;AS_SB_TABLE=0,1|0,2|0,0;AS_VarDP=1|2|0;BaseQRankSum=0.967;DP=3;FILTERED_HAPS=0;MQRankSum=-0.967;QUALapprox=73;RAW_GT_COUNT=0,1,0;RAW_MQandDP=7892,3;ReadPosRankSum=0;TREE_SCORE=0.849228;VarDP=3	GT:AD:DP:GQ:PL:SB	0/1:1,2,0:3:36:73,0,36,84,42,117:0,1,0,2
+chr1	853877	.	G	<NON_REF>	.	.	END=854270	GT:DP:GQ	0/0:3:0
+chr1	854271	.	A	G,<NON_REF>	35.48	.	ASSEMBLED_HAPS=2;AS_QUALapprox=|45|0;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|324.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|0,0|0,0;AS_VarDP=0|0|0;DP=1;FILTERED_HAPS=0;QUALapprox=45;RAW_GT_COUNT=0,0,1;RAW_MQandDP=324,1;TREE_SCORE=0.97165;VarDP=1	GT:AD:DP:GQ:PL:SB	1/1:0,1,0:1:3:45,3,0,45,3,45:0,0,0,1
+chr1	854272	.	T	<NON_REF>	.	.	END=864082	GT:DP:GQ	0/0:0:0
+chr1	864083	.	T	C,<NON_REF>	35.48	.	ASSEMBLED_HAPS=2;AS_QUALapprox=|45|0;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|676.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|0,0|0,0;AS_VarDP=0|0|0;DP=1;FILTERED_HAPS=0;QUALapprox=45;RAW_GT_COUNT=0,0,1;RAW_MQandDP=676,1;TREE_SCORE=0.972834;VarDP=1	GT:AD:DP:GQ:PL:SB	1/1:0,1,0:1:3:45,3,0,45,3,45:0,0,0,1
+chr1	864084	.	A	<NON_REF>	.	.	END=864445	GT:DP:GQ	0/0:4:0
+chr1	864446	.	C	<NON_REF>	.	.	END=864455	GT:DP:GQ	0/0:7:20
+chr1	864456	.	T	<NON_REF>	.	.	END=864514	GT:DP:GQ	0/0:6:0
+chr1	864515	.	G	<NON_REF>	.	.	END=864524	GT:DP:GQ	0/0:7:20
+chr1	864525	.	A	<NON_REF>	.	.	END=864528	GT:DP:GQ	0/0:7:0
+chr1	864529	.	C	<NON_REF>	.	.	END=864550	GT:DP:GQ	0/0:8:20
+chr1	864551	.	A	<NON_REF>	.	.	END=864551	GT:DP:GQ	0/0:7:0
+chr1	864552	.	T	<NON_REF>	.	.	END=864575	GT:DP:GQ	0/0:7:20
+chr1	864576	.	C	<NON_REF>	.	.	END=864576	GT:DP:GQ	0/0:7:0
+chr1	864577	.	T	<NON_REF>	.	.	END=864607	GT:DP:GQ	0/0:7:20
+chr1	864608	.	C	<NON_REF>	.	.	END=864609	GT:DP:GQ	0/0:7:0
+chr1	864610	.	T	<NON_REF>	.	.	END=864626	GT:DP:GQ	0/0:7:20
+chr1	864627	.	T	C,<NON_REF>	80.02	.	ASSEMBLED_HAPS=2;AS_QUALapprox=|94|0;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|11044.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|3,4|0,0;AS_VarDP=0|7|0;DP=7;FILTERED_HAPS=0;QUALapprox=94;RAW_GT_COUNT=0,0,1;RAW_MQandDP=11044,7;TREE_SCORE=0.996562;VarDP=7	GT:AD:DP:GQ:PL:SB	1/1:0,7,0:7:21:94,21,0,315,21,94:0,0,3,4
+chr1	864628	.	T	<NON_REF>	.	.	END=864658	GT:DP:GQ	0/0:7:20
+chr1	864659	.	A	<NON_REF>	.	.	END=886481	GT:DP:GQ	0/0:4:0
+chr1	886482	.	CACAGCAGCTGTGCTGTGTT	C,<NON_REF>	67.60	.	ASSEMBLED_HAPS=54;AS_QUALapprox=|75|0;AS_RAW_BaseQRankSum=|0.0,1|NaN;AS_RAW_MQ=3600.00|10009.00|0.00;AS_RAW_MQRankSum=|-0.4,1|NaN;AS_RAW_ReadPosRankSum=|-1.2,1|NaN;AS_SB_TABLE=1,0|3,0|0,0;AS_VarDP=1|3|0;BaseQRankSum=0;DP=4;FILTERED_HAPS=43;MQRankSum=-0.319;QUALapprox=75;RAW_GT_COUNT=0,1,0;RAW_MQandDP=13609,4;ReadPosRankSum=-1.15;TREE_SCORE=0.963101;VarDP=4	GT:AD:DP:GQ:PL:SB	0/1:1,3,0:4:33:75,0,33,112,42,117:1,0,3,0
+chr1	886502	.	A	<NON_REF>	.	.	END=886506	GT:DP:GQ	0/0:4:0
+chr1	886507	.	A	G,<NON_REF>	73.13	.	ASSEMBLED_HAPS=54;AS_QUALapprox=|87|0;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|13609.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|4,0|0,0;AS_VarDP=0|4|0;DP=4;FILTERED_HAPS=43;QUALapprox=87;RAW_GT_COUNT=0,0,1;RAW_MQandDP=13609,4;TREE_SCORE=0.997634;VarDP=4	GT:AD:DP:GQ:PL:SB	1/1:0,4,0:4:12:87,12,0,166,12,87:0,0,4,0
+chr1	886508	.	A	<NON_REF>	.	.	END=886567	GT:DP:GQ	0/0:4:0
+chr1	886568	.	T	C,<NON_REF>	70.83	.	ASSEMBLED_HAPS=8;AS_QUALapprox=|84|0;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|10800.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|3,0|0,0;AS_VarDP=0|3|0;DP=3;FILTERED_HAPS=4;QUALapprox=84;RAW_GT_COUNT=0,0,1;RAW_MQandDP=10800,3;TREE_SCORE=0.99842;VarDP=3	GT:AD:DP:GQ:PL:SB	1/1:0,3,0:3:9:84,9,0,135,9,84:0,0,3,0
+chr1	886569	.	G	<NON_REF>	.	.	END=910957	GT:DP:GQ	0/0:2:0
+chr1	910958	.	A	G,<NON_REF>	69.31	.	ASSEMBLED_HAPS=29;AS_QUALapprox=|81|0;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|7200.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|0,0|0,0;AS_VarDP=0|2|0;DP=2;FILTERED_HAPS=14;QUALapprox=81;RAW_GT_COUNT=0,0,1;RAW_MQandDP=7200,2;TREE_SCORE=0.996788;VarDP=2	GT:AD:DP:GQ:PL:SB	1/1:0,2,0:2:6:81,6,0,90,6,81:0,0,0,2
+chr1	910959	.	C	<NON_REF>	.	.	END=911017	GT:DP:GQ	0/0:3:0
+chr1	911018	.	G	A,<NON_REF>	73.13	.	ASSEMBLED_HAPS=53;AS_QUALapprox=|87|0;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|14400.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|1,3|0,0;AS_VarDP=0|4|0;DP=4;FILTERED_HAPS=18;QUALapprox=87;RAW_GT_COUNT=0,0,1;RAW_MQandDP=14400,4;TREE_SCORE=0.99858;VarDP=4	GT:AD:DP:GQ:PL:SB	1/1:0,4,0:4:12:87,12,0,180,12,87:0,0,1,3
+chr1	911019	.	C	<NON_REF>	.	.	END=911084	GT:DP:GQ	0/0:5:0
+chr1	911085	.	C	T,CTG,<NON_REF>	85.05	.	ASSEMBLED_HAPS=92;AS_QUALapprox=|72|30|0;AS_RAW_BaseQRankSum=|0.0,1|0.6,1|NaN;AS_RAW_MQ=3600.00|7200.00|3600.00|0.00;AS_RAW_MQRankSum=|0.0,1|0.0,1|NaN;AS_RAW_ReadPosRankSum=|0.0,1|0.6,1|NaN;AS_SB_TABLE=1,0|0,2|0,1|0,0;AS_VarDP=1|2|1|0;BaseQRankSum=0.319;DP=5;FILTERED_HAPS=66;MQRankSum=0;QUALapprox=102;RAW_GT_COUNT=0,0,1;RAW_MQandDP=18000,5;ReadPosRankSum=0.319;TREE_SCORE=0.970667;VarDP=4	GT:AD:DP:GQ:PL:SB	1/2:1,2,1,0:4:30:102,30,36,72,0,75,114,42,84,117:1,0,0,3
+chr1	911086	.	C	<NON_REF>	.	.	END=911162	GT:DP:GQ	0/0:4:0
+chr1	911163	.	G	T,<NON_REF>	64.74	.	ASSEMBLED_HAPS=92;AS_QUALapprox=|72|0;AS_RAW_BaseQRankSum=|0.9,1|NaN;AS_RAW_MQ=3600.00|7200.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|0.0,1|NaN;AS_SB_TABLE=1,0|0,2|0,0;AS_VarDP=1|2|0;BaseQRankSum=0.967;DP=4;FILTERED_HAPS=66;MQRankSum=0;QUALapprox=72;RAW_GT_COUNT=0,1,0;RAW_MQandDP=14400,4;ReadPosRankSum=0;TREE_SCORE=0.996968;VarDP=3	GT:AD:DP:GQ:PL:SB	0/1:1,2,0:3:6:72,0,6,84,12,87:1,0,0,2
+chr1	911164	.	C	<NON_REF>	.	.	END=911219	GT:DP:GQ	0/0:5:0
+chr1	911220	.	CT	C,<NON_REF>	75.92	.	ASSEMBLED_HAPS=92;AS_QUALapprox=|90|0;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|18000.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|3,2|0,0;AS_VarDP=0|5|0;DP=6;FILTERED_HAPS=66;QUALapprox=90;RAW_GT_COUNT=0,0,1;RAW_MQandDP=21600,6;TREE_SCORE=0.977651;VarDP=5	GT:AD:DP:GQ:PL:SB	1/1:0,5,0:5:15:90,15,0,150,15,90:0,0,3,2
+chr1	911222	.	T	<NON_REF>	.	.	END=911427	GT:DP:GQ	0/0:6:0
+chr1	911428	.	C	T,<NON_REF>	70.83	.	ASSEMBLED_HAPS=16;AS_QUALapprox=|84|0;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|10800.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|2,1|0,0;AS_VarDP=0|3|0;DP=3;FILTERED_HAPS=0;QUALapprox=84;RAW_GT_COUNT=0,0,1;RAW_MQandDP=10800,3;TREE_SCORE=0.998421;VarDP=3	GT:AD:DP:GQ:PL:SB	1/1:0,3,0:3:9:84,9,0,135,9,84:0,0,2,1
+chr1	911429	.	G	<NON_REF>	.	.	END=911483	GT:DP:GQ	0/0:3:0
+chr1	911484	.	G	C,<NON_REF>	69.31	.	ASSEMBLED_HAPS=16;AS_QUALapprox=|81|0;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|7200.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|0,0|0,0;AS_VarDP=0|2|0;DP=2;FILTERED_HAPS=0;QUALapprox=81;RAW_GT_COUNT=0,0,1;RAW_MQandDP=7200,2;TREE_SCORE=0.996826;VarDP=2	GT:AD:DP:GQ:PL:SB	1/1:0,2,0:2:6:81,6,0,90,6,81:0,0,1,1
+chr1	911485	.	A	<NON_REF>	.	.	END=911488	GT:DP:GQ	0/0:2:0
+chr1	911489	.	G	GA,<NON_REF>	35.44	.	ASSEMBLED_HAPS=16;AS_QUALapprox=|45|0;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|3600.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|0,0|0,0;AS_VarDP=0|0|0;DP=2;FILTERED_HAPS=0;QUALapprox=45;RAW_GT_COUNT=0,0,1;RAW_MQandDP=7200,2;TREE_SCORE=0.336352;VarDP=1	GT:AD:DP:GQ:PGT:PID:PL:PS:SB	1|1:0,1,0:1:3:0|1:911489_G_GA:45,3,0,45,3,45:911489:0,0,1,0
+chr1	911490	.	T	<NON_REF>	.	.	END=911495	GT:DP:GQ	0/0:1:0
+chr1	911496	.	TG	T,<NON_REF>	35.44	.	ASSEMBLED_HAPS=16;AS_QUALapprox=|45|0;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|3600.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|0,0|0,0;AS_VarDP=0|0|0;DP=1;FILTERED_HAPS=0;QUALapprox=45;RAW_GT_COUNT=0,0,1;RAW_MQandDP=3600,1;TREE_SCORE=0.401471;VarDP=1	GT:AD:DP:GQ:PGT:PID:PL:PS:SB	1|1:0,1,0:1:3:0|1:911489_G_GA:45,3,0,45,3,45:911489:0,0,1,0
+chr1	911498	.	G	<NON_REF>	.	.	END=918107	GT:DP:GQ	0/0:0:0
+chr1	918108	.	G	A,<NON_REF>	35.48	.	ASSEMBLED_HAPS=2;AS_QUALapprox=|45|0;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|3600.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|0,0|0,0;AS_VarDP=0|0|0;DP=1;FILTERED_HAPS=0;QUALapprox=45;RAW_GT_COUNT=0,0,1;RAW_MQandDP=3600,1;TREE_SCORE=0.98105;VarDP=1	GT:AD:DP:GQ:PL:SB	1/1:0,1,0:1:3:45,3,0,45,3,45:0,0,1,0
+chr1	918109	.	G	<NON_REF>	.	.	END=918787	GT:DP:GQ	0/0:3:0
+chr1	918788	.	C	T,<NON_REF>	35.48	.	ASSEMBLED_HAPS=2;AS_QUALapprox=|45|0;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|3600.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|0,0|0,0;AS_VarDP=0|0|0;DP=1;FILTERED_HAPS=0;QUALapprox=45;RAW_GT_COUNT=0,0,1;RAW_MQandDP=3600,1;TREE_SCORE=0.983445;VarDP=1	GT:AD:DP:GQ:PL:SB	1/1:0,1,0:1:3:45,3,0,45,3,45:0,0,1,0
+chr1	918789	.	A	<NON_REF>	.	.	END=922447	GT:DP:GQ	0/0:0:0
+chr1	922448	.	A	G,<NON_REF>	66.64	.	ASSEMBLED_HAPS=8;AS_QUALapprox=|74|0;AS_RAW_BaseQRankSum=|-0.5,1|NaN;AS_RAW_MQ=3600.00|7200.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|-1.0,1|NaN;AS_SB_TABLE=0,1|1,1|0,0;AS_VarDP=1|2|0;BaseQRankSum=-0.431;DP=3;FILTERED_HAPS=4;MQRankSum=0;QUALapprox=74;RAW_GT_COUNT=0,1,0;RAW_MQandDP=10800,3;ReadPosRankSum=-0.967;TREE_SCORE=0.998366;VarDP=3	GT:AD:DP:GQ:PL:SB	0/1:1,2,0:3:36:74,0,36,77,42,117:0,1,1,1
+chr1	922449	.	G	<NON_REF>	.	.	END=922672	GT:DP:GQ	0/0:5:0
+chr1	922673	.	T	<NON_REF>	.	.	END=922678	GT:DP:GQ	0/0:7:20
+chr1	922679	.	G	<NON_REF>	.	.	END=922679	GT:DP:GQ	0/0:6:0
+chr1	922680	.	A	<NON_REF>	.	.	END=922680	GT:DP:GQ	0/0:7:20
+chr1	922681	.	G	<NON_REF>	.	.	END=922681	GT:DP:GQ	0/0:6:0
+chr1	922682	.	C	<NON_REF>	.	.	END=922684	GT:DP:GQ	0/0:7:20
+chr1	922685	.	T	<NON_REF>	.	.	END=922686	GT:DP:GQ	0/0:7:0
+chr1	922687	.	C	<NON_REF>	.	.	END=922690	GT:DP:GQ	0/0:7:20
+chr1	922691	.	C	<NON_REF>	.	.	END=922701	GT:DP:GQ	0/0:7:0
+chr1	922702	.	C	<NON_REF>	.	.	END=922711	GT:DP:GQ	0/0:7:20
+chr1	922712	.	T	<NON_REF>	.	.	END=950541	GT:DP:GQ	0/0:4:0
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/actual.NA12878.rb.g.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/actual.NA12878.rb.g.vcf.idx
new file mode 100644
index 00000000000..ea94cd86b68
Binary files /dev/null and b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/actual.NA12878.rb.g.vcf.idx differ
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/actual.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/actual.vcf
new file mode 100644
index 00000000000..213549fd5bf
--- /dev/null
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/actual.vcf
@@ -0,0 +1,3467 @@
+##fileformat=VCFv4.2
+##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
+##FILTER=<ID=ExcessHet,Description="ExcessHet > 54.69">
+##FILTER=<ID=LowQual,Description="Low quality">
+##FILTER=<ID=PASS,Description="All filters passed">
+##FILTER=<ID=VQSRTrancheINDEL95.00to96.00,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -1.7337 <= x < -0.3732">
+##FILTER=<ID=VQSRTrancheINDEL96.00to97.00,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -2.2629 <= x < -1.7337">
+##FILTER=<ID=VQSRTrancheINDEL97.00to99.00,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -2.6642 <= x < -2.2629">
+##FILTER=<ID=VQSRTrancheINDEL99.00to99.50,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -3.0744 <= x < -2.6642">
+##FILTER=<ID=VQSRTrancheINDEL99.50to99.90,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -6.999 <= x < -3.0744">
+##FILTER=<ID=VQSRTrancheINDEL99.90to99.95,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -12.3215 <= x < -6.999">
+##FILTER=<ID=VQSRTrancheINDEL99.95to100.00+,Description="Truth sensitivity tranche level for INDEL model at VQS Lod < -24539.8179">
+##FILTER=<ID=VQSRTrancheINDEL99.95to100.00,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -24539.8179 <= x < -12.3215">
+##FILTER=<ID=VQSRTrancheSNP99.00to99.90+,Description="Truth sensitivity tranche level for SNP model at VQS Lod < -10.0">
+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
+##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">
+##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
+##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
+##GATKCommandLine=<ID=ApplyVQSR,CommandLine="ApplyVQSR --recal-file /cromwell_root/broad-gotc-dev-cromwell-execution/TestJointGenotyping/dd7389a8-f924-4db4-8352-6bda6fdfbbd9/call-JointGenotyping/JointGenotyping/da8e4e6f-1a68-49fb-9fdf-eea25615d950/call-IndelsVariantRecalibrator/small_callset_low_threshold.indels.recal --tranches-file /cromwell_root/broad-gotc-dev-cromwell-execution/TestJointGenotyping/dd7389a8-f924-4db4-8352-6bda6fdfbbd9/call-JointGenotyping/JointGenotyping/da8e4e6f-1a68-49fb-9fdf-eea25615d950/call-IndelsVariantRecalibrator/small_callset_low_threshold.indels.tranches --output tmp.indel.recalibrated.vcf --truth-sensitivity-filter-level 95.0 --use-allele-specific-annotations true --mode INDEL --variant /cromwell_root/broad-gotc-dev-cromwell-execution/TestJointGenotyping/dd7389a8-f924-4db4-8352-6bda6fdfbbd9/call-JointGenotyping/JointGenotyping/da8e4e6f-1a68-49fb-9fdf-eea25615d950/call-HardFilterAndMakeSitesOnlyVcf/shard-0/small_callset_low_threshold.0.variant_filtered.vcf.gz --create-output-variant-index true --ignore-all-filters false --exclude-filtered false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false",Version="4.6.0.0",Date="July 12, 2024 at 2:59:21 PM GMT">
+##GATKCommandLine=<ID=SelectVariants,CommandLine="SelectVariants --output /Users/mshand/Github/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/actual.vcf --variant actual_small_no_nocalls.vcf.gz --intervals chr1:1-945670 --apply-jexl-filters-first false --invertSelect false --exclude-non-variants false --exclude-filtered false --preserve-alleles false --remove-unused-alternates false --restrict-alleles-to ALL --keep-original-ac false --keep-original-dp false --mendelian-violation false --invert-mendelian-violation false --mendelian-violation-qual-threshold 0.0 --select-random-fraction 1.0 --remove-fraction-genotypes 0.0 --ignore-non-ref-in-types false --fully-decode false --max-indel-size 2147483647 --min-indel-size 0 --max-filtered-genotypes 2147483647 --min-filtered-genotypes 0 --max-fraction-filtered-genotypes 1.0 --min-fraction-filtered-genotypes 0.0 --max-nocall-number 2147483647 --max-nocall-fraction 1.0 --set-filtered-gt-to-nocall false --allow-nonoverlapping-command-line-samples false --suppress-reference-path false --fail-on-unsorted-genotype false --genomicsdb-max-alternate-alleles 50 --call-genotypes false --genomicsdb-use-bcf-codec false --genomicsdb-shared-posixfs-optimizations false --genomicsdb-use-gcs-hdfs-connector false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false",Version="4.6.0.0-19-g6a6872f-SNAPSHOT",Date="July 30, 2024 at 4:28:44 PM EDT">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=AS_BaseQRankSum,Number=A,Type=Float,Description="allele specific Z-score from Wilcoxon rank sum test of each Alt Vs. Ref base qualities">
+##INFO=<ID=AS_FS,Number=A,Type=Float,Description="allele specific phred-scaled p-value using Fisher's exact test to detect strand bias of each alt allele">
+##INFO=<ID=AS_FilterStatus,Number=A,Type=String,Description="Filter status for each allele, as assessed by ApplyVQSR. Note that the VCF filter field will reflect the most lenient/sensitive status across all alleles.">
+##INFO=<ID=AS_InbreedingCoeff,Number=A,Type=Float,Description="Allele-specific inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
+##INFO=<ID=AS_MQ,Number=A,Type=Float,Description="Allele-specific RMS Mapping Quality">
+##INFO=<ID=AS_MQRankSum,Number=A,Type=Float,Description="Allele-specific Mapping Quality Rank Sum">
+##INFO=<ID=AS_QD,Number=A,Type=Float,Description="Allele-specific Variant Confidence/Quality by Depth">
+##INFO=<ID=AS_QUALapprox,Number=1,Type=String,Description="Allele-specific QUAL approximations">
+##INFO=<ID=AS_RAW_BaseQRankSum,Number=1,Type=String,Description="raw data for allele specific rank sum test of base qualities">
+##INFO=<ID=AS_RAW_MQ,Number=1,Type=String,Description="Allele-specfic raw data for RMS Mapping Quality">
+##INFO=<ID=AS_RAW_MQRankSum,Number=1,Type=String,Description="Allele-specfic raw data for Mapping Quality Rank Sum">
+##INFO=<ID=AS_RAW_ReadPosRankSum,Number=1,Type=String,Description="allele specific raw data for rank sum test of read position bias">
+##INFO=<ID=AS_ReadPosRankSum,Number=A,Type=Float,Description="allele specific Z-score from Wilcoxon rank sum test of each Alt vs. Ref read position bias">
+##INFO=<ID=AS_SB_TABLE,Number=1,Type=String,Description="Allele-specific forward/reverse read counts for strand bias tests">
+##INFO=<ID=AS_SOR,Number=A,Type=Float,Description="Allele specific strand Odds Ratio of 2x|Alts| contingency table to detect allele specific strand bias">
+##INFO=<ID=AS_VQSLOD,Number=A,Type=String,Description="For each alt allele, the log odds of being a true variant versus being false under the trained gaussian mixture model">
+##INFO=<ID=AS_VarDP,Number=1,Type=String,Description="Allele-specific (informative) depth over variant genotypes; effectively sum of ADs">
+##INFO=<ID=AS_culprit,Number=A,Type=String,Description="For each alt allele, the annotation which was the worst performing in the Gaussian mixture model, likely the reason why the variant was filtered out">
+##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
+##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
+##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
+##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
+##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
+##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
+##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
+##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
+##INFO=<ID=MQ_DP,Number=1,Type=Integer,Description="Depth over variant samples for better MQ calculation (deprecated -- use RAW_MQandDP instead.">
+##INFO=<ID=NEGATIVE_TRAIN_SITE,Number=0,Type=Flag,Description="This variant was used to build the negative training set of bad variants">
+##INFO=<ID=POSITIVE_TRAIN_SITE,Number=0,Type=Flag,Description="This variant was used to build the positive training set of good variants">
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+##INFO=<ID=culprit,Number=1,Type=String,Description="The annotation which was the worst performing in the Gaussian mixture model, likely the reason why the variant was filtered out">
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+##source=SelectVariants
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	CHMI_CHMI3_Nex1	NA12878	NA12891	NA12892	NA19238	NA20845	NA20846	NA20847	NA20849	NA20850	NA20851	NA20852	NA20853	NA20854	NA20856	NA20858	NA20859	NA20861	NA20862	NA20866	NA20869	NA20870	NA20871	NA20872	NA20873	NA20874	NA20875	NA20876	NA20877	NA20878	NA20881	NA20885	NA20886	NA20887	NA20888	NA20889	NA20890	NA20891	NA20892	NA20893	NA20894	NA20895	NA20896	NA20897	NA20898	NA20899	NA20901	NA20902	NA20903	NA20904	NA20905	NA20906	NA20908	NA20910	NA20911	NA21086	NA21087	NA21088	NA21093	NA21095	NA21114	NA21124	NA21126	NA21129	NA21137
+chr1	186475	.	G	T	121.70	PASS	AC=1;AF=7.692e-03;AN=130;AS_BaseQRankSum=-0.200;AS_FS=0.000;AS_FilterStatus=PASS;AS_InbreedingCoeff=-0.0120;AS_MQ=26.33;AS_MQRankSum=-0.500;AS_QD=3.94;AS_ReadPosRankSum=0.400;AS_SOR=0.601;AS_VQSLOD=-4.8149;AS_culprit=AS_MQ;BaseQRankSum=-1.560e-01;DP=2012;ExcessHet=0.0000;FS=0.000;InbreedingCoeff=-0.0124;MLEAC=1;MLEAF=7.692e-03;MQ=27.51;MQRankSum=-4.110e-01;QD=3.93;ReadPosRankSum=0.452;SOR=0.601	GT:AD:DP:GQ:PL	0/0:183,0:183:60	0/0:257,0:257:60	0/0:253,0:253:60	0/0:213,0:213:60	0/0:17,0:17:40	0/0:14,0:14:30	0/0:23,0:23:60	0/0:25,0:25:60	0/0:10,0:10:20	0/0:7,0:7:10	0/0:21,0:21:60	0/0:23,0:23:60	0/0:13,0:13:30	0/0:15,0:15:30	0/0:18,0:18:40	0/0:15,0:15:40	0/0:23,0:23:60	0/1:23,8:31:99:140,0,556	0/0:15,0:15:30	0/0:11,0:11:30	0/0:35,0:35:60	0/0:23,0:23:50	0/0:15,0:15:30	0/0:26,0:26:60	0/0:30,0:30:60	0/0:29,0:29:60	0/0:29,0:29:60	0/0:15,0:15:30	0/0:14,0:14:30	0/0:20,0:20:50	0/0:9,0:9:20	0/0:14,0:14:30	0/0:12,0:12:30	0/0:29,0:29:60	0/0:4,0:4:10	0/0:6,0:6:10	0/0:22,0:22:40	0/0:33,0:33:60	0/0:9,0:9:20	0/0:14,0:14:30	0/0:29,0:29:60	0/0:15,0:15:30	0/0:5,0:5:10	0/0:11,0:11:30	0/0:26,0:26:60	0/0:15,0:15:30	0/0:8,0:8:20	0/0:10,0:10:20	0/0:15,0:15:30	0/0:23,0:23:50	0/0:23,0:23:50	0/0:15,0:15:40	0/0:30,0:30:60	0/0:5,0:5:10	0/0:20,0:20:50	0/0:13,0:13:30	0/0:19,0:19:40	0/0:18,0:18:40	0/0:19,0:19:20	0/0:15,0:15:30	0/0:18,0:18:50	0/0:7,0:7:20	0/0:33,0:33:60	0/0:14,0:14:30	0/0:31,0:31:60
+chr1	187471	.	A	C	60.64	VQSRTrancheSNP99.00to99.90+	AC=2;AF=0.015;AN=130;AS_BaseQRankSum=3.100;AS_FS=100.350;AS_FilterStatus=VQSRTrancheSNP99.00to99.90+;AS_InbreedingCoeff=-0.0159;AS_MQ=28.18;AS_MQRankSum=-3.400;AS_QD=0.13;AS_ReadPosRankSum=-5.650;AS_SOR=6.803;AS_VQSLOD=-93.7153;AS_culprit=AS_FS;BaseQRankSum=3.47;DP=2943;ExcessHet=0.0338;FS=100.350;InbreedingCoeff=-0.0159;MLEAC=1;MLEAF=7.692e-03;MQ=32.38;MQRankSum=-3.205e+00;QD=0.12;ReadPosRankSum=-4.542e+00;SOR=6.803	GT:AD:DP:GQ:PL	0/0:242,0:242:10	0/1:197,31:228:77:77,0,8939	0/1:229,29:258:12:12,0,8067	0/0:283,0:283:60	0/0:27,0:27:60	0/0:26,0:26:60	0/0:35,0:35:60	0/0:29,0:29:60	0/0:34,0:34:60	0/0:40,0:40:60	0/0:31,0:31:60	0/0:32,0:32:60	0/0:27,0:27:60	0/0:28,0:28:60	0/0:29,0:29:60	0/0:27,0:27:60	0/0:37,0:37:60	0/0:32,0:32:60	0/0:37,0:37:60	0/0:29,0:29:60	0/0:29,0:29:60	0/0:32,0:32:60	0/0:28,0:28:60	0/0:26,0:26:60	0/0:32,0:32:60	0/0:32,0:32:60	0/0:49,0:49:60	0/0:29,0:29:60	0/0:27,0:27:60	0/0:28,0:28:60	0/0:33,0:33:60	0/0:31,0:31:60	0/0:33,0:33:60	0/0:30,0:30:60	0/0:31,0:31:60	0/0:29,0:29:60	0/0:34,0:34:60	0/0:28,0:28:60	0/0:29,0:29:60	0/0:51,0:51:60	0/0:30,0:30:60	0/0:29,0:29:60	0/0:31,0:31:60	0/0:32,0:32:60	0/0:33,0:33:60	0/0:58,0:58:60	0/0:27,0:27:60	0/0:32,0:32:60	0/0:38,0:38:60	0/0:28,0:28:60	0/0:32,0:32:60	0/0:31,0:31:60	0/0:28,0:28:60	0/0:28,0:28:60	0/0:31,0:31:60	0/0:28,0:28:60	0/0:29,0:29:60	0/0:31,0:31:60	0/0:28,0:28:60	0/0:28,0:28:60	0/0:31,0:31:60	0/0:30,0:30:60	0/0:42,0:42:60	0/0:27,0:27:60	0/0:29,0:29:60
+chr1	187485	.	G	A	97359.39	ExcessHet	AC=74;AF=0.569;AN=130;AS_BaseQRankSum=0.000;AS_FS=4.039;AS_InbreedingCoeff=-0.7568;AS_MQ=29.24;AS_MQRankSum=-0.400;AS_QD=17.72;AS_ReadPosRankSum=0.050;AS_SOR=0.989;BaseQRankSum=0.058;DP=5503;ExcessHet=100.7690;FS=4.039;InbreedingCoeff=-0.7568;MLEAC=74;MLEAF=0.569;MQ=29.46;MQRankSum=-3.180e-01;QD=17.72;ReadPosRankSum=0.110;SOR=0.991	GT:AD:DP:GQ:PGT:PID:PL	0/1:33,235:271:99:.:.:7017,0,616	1/1:9,236:245:99:.:.:7627,450,0	0/1:131,138:269:99:.:.:2911,0,3374	0/1:93,207:300:99:.:.:6270,0,1857	0/1:18,53:71:99:0|1:187485_G_A:1410,0,246	0/1:18,41:59:99:0|1:187485_G_A:1145,0,299	0/1:44,46:90:99:.:.:1011,0,919	0/1:26,20:46:99:0|1:187485_G_A:598,0,582	0/1:53,49:102:99:0|1:187485_G_A:1184,0,1070	0/1:28,63:91:99:0|1:187485_G_A:2155,0,486	0/1:19,37:56:99:0|1:187485_G_A:1017,0,356	0/1:12,75:87:51:.:.:2110,0,51	0/1:32,49:81:99:0|1:187485_G_A:1489,0,616	0/1:55,35:90:99:.:.:676,0,1231	0/1:25,29:54:99:.:.:666,0,511	1/1:0,27:27:81:.:.:751,81,0	0/1:36,26:62:99:.:.:519,0,810	0/1:35,55:90:99:0|1:187485_G_A:1513,0,681	0/1:26,48:74:99:0|1:187485_G_A:1506,0,471	0/1:24,50:74:99:0|1:187485_G_A:1421,0,411	0/1:23,27:50:99:0|1:187485_G_A:822,0,471	0/1:16,63:79:99:.:.:1442,0,168	0/1:22,61:83:99:0|1:187485_G_A:2141,0,345	0/1:72,15:87:99:.:.:162,0,1680	0/1:38,34:72:99:.:.:736,0,816	0/1:37,41:78:99:0|1:187485_G_A:1062,0,750	0/1:22,70:92:99:0|1:187485_G_A:1904,0,324	0/1:26,77:103:99:0|1:187485_G_A:2415,0,387	1/1:0,31:31:93:.:.:841,93,0	0/1:25,34:59:99:.:.:710,0,515	1/1:0,51:51:99:1|1:187485_G_A:1640,153,0	0/1:43,39:82:99:.:.:806,0,923	1/1:4,57:61:84:.:.:1436,84,0	0/1:46,46:92:99:.:.:958,0,977	0/1:24,43:67:99:0|1:187485_G_A:1301,0,460	0/1:19,20:39:99:.:.:452,0,396	0/1:42,36:78:99:.:.:765,0,870	0/1:38,38:76:99:.:.:802,0,786	0/1:18,58:76:99:0|1:187485_G_A:1530,0,265	0/1:52,25:77:99:.:.:537,0,1213	0/1:39,25:64:99:0|1:187485_G_A:794,0,794	0/1:28,110:138:99:0|1:187485_G_A:3079,0,354	0/1:40,18:58:99:.:.:320,0,904	0/1:17,52:69:99:0|1:187485_G_A:1338,0,262	0/1:10,45:55:93:.:.:1053,0,93	0/1:34,41:75:99:0|1:187485_G_A:1180,0,705	1/1:0,39:39:99:1|1:187485_G_A:1489,117,0	1/1:0,33:33:99:.:.:861,99,0	0/1:13,61:74:99:0|1:187485_G_A:1602,0,131	0/1:25,46:71:99:0|1:187485_G_A:1203,0,459	0/1:26,43:69:99:0|1:187485_G_A:1472,0,494	1/1:0,89:89:99:.:.:2606,267,0	0/1:42,51:93:99:0|1:187485_G_A:1308,0,866	0/1:14,68:82:99:.:.:1692,0,134	0/1:40,48:88:99:.:.:1016,0,787	0/1:27,17:44:99:.:.:321,0,606	0/1:18,63:81:99:0|1:187485_G_A:1650,0,240	0/1:33,36:69:99:.:.:977,0,673	0/1:20,41:61:99:.:.:1034,0,336	0/1:25,22:47:99:.:.:458,0,529	0/1:24,37:61:99:.:.:807,0,473	1/1:0,39:39:99:.:.:1071,117,0	0/1:55,93:148:99:.:.:2652,0,1049	0/1:37,44:81:99:0|1:187485_G_A:1163,0,735	0/1:65,32:97:99:.:.:550,0,1508
+chr1	187499	.	A	G	296.62	VQSRTrancheSNP99.00to99.90+	AC=1;AF=7.692e-03;AN=130;AS_BaseQRankSum=1.700;AS_FS=93.945;AS_FilterStatus=VQSRTrancheSNP99.00to99.90+;AS_InbreedingCoeff=-0.0078;AS_MQ=28.65;AS_MQRankSum=0.400;AS_QD=1.03;AS_ReadPosRankSum=1.300;AS_SOR=2.365;AS_VQSLOD=-73.0456;AS_culprit=AS_FS;BaseQRankSum=1.75;DP=2977;ExcessHet=0.0000;FS=93.945;InbreedingCoeff=-0.0078;MLEAC=1;MLEAF=7.692e-03;MQ=28.19;MQRankSum=0.454;QD=1.03;ReadPosRankSum=1.37;SOR=2.365	GT:AD:DP:GQ:PL	0/1:255,32:287:99:315,0,10200	0/0:193,0:193:60	0/0:178,0:178:60	0/0:203,0:203:60	0/0:37,0:37:60	0/0:33,0:33:60	0/0:31,0:31:60	0/0:36,0:36:60	0/0:37,0:37:60	0/0:34,0:34:60	0/0:36,0:36:60	0/0:38,0:38:60	0/0:39,0:39:60	0/0:36,0:36:60	0/0:38,0:38:60	0/0:34,0:34:60	0/0:34,0:34:60	0/0:33,0:33:60	0/0:34,0:34:60	0/0:34,0:34:60	0/0:38,0:38:60	0/0:34,0:34:60	0/0:34,0:34:60	0/0:32,0:32:60	0/0:36,0:36:60	0/0:32,0:32:60	0/0:36,0:36:60	0/0:34,0:34:60	0/0:34,0:34:60	0/0:33,0:33:60	0/0:33,0:33:60	0/0:33,0:33:60	0/0:35,0:35:60	0/0:38,0:38:60	0/0:34,0:34:60	0/0:39,0:39:60	0/0:33,0:33:60	0/0:37,0:37:60	0/0:36,0:36:60	0/0:34,0:34:60	0/0:34,0:34:60	0/0:33,0:33:60	0/0:35,0:35:60	0/0:35,0:35:60	0/0:32,0:32:60	0/0:33,0:33:60	0/0:42,0:42:60	0/0:37,0:37:60	0/0:31,0:31:60	0/0:35,0:35:60	0/0:33,0:33:60	0/0:31,0:31:60	0/0:36,0:36:60	0/0:33,0:33:60	0/0:30,0:30:60	0/0:36,0:36:60	0/0:30,0:30:60	0/0:32,0:32:60	0/0:39,0:39:60	0/0:33,0:33:60	0/0:33,0:33:60	0/0:38,0:38:60	0/0:37,0:37:60	0/0:33,0:33:60	0/0:35,0:35:60
+chr1	805887	rs201849753	T	C	2153.83	PASS	AC=4;AF=0.031;AN=130;AS_BaseQRankSum=-0.550;AS_FS=2.750;AS_FilterStatus=PASS;AS_InbreedingCoeff=-0.0317;AS_MQ=29.60;AS_MQRankSum=-0.850;AS_QD=9.32;AS_ReadPosRankSum=-0.100;AS_SOR=0.919;AS_VQSLOD=-3.4000;AS_culprit=AS_MQ;BaseQRankSum=-1.950e-01;DB;DP=2215;ExcessHet=0.2060;FS=2.750;InbreedingCoeff=-0.0317;MLEAC=4;MLEAF=0.031;MQ=31.15;MQRankSum=0.211;QD=9.32;ReadPosRankSum=0.525;SOR=0.919	GT:AD:DP:GQ:PL	0/0:22,0:22:50	0/0:30,0:30:60	0/0:33,0:33:60	0/0:28,0:28:60	0/0:36,0:36:60	0/0:38,0:38:60	0/0:34,0:34:60	0/0:32,0:32:60	0/0:36,0:36:60	0/0:35,0:35:60	0/0:35,0:35:60	0/0:32,0:32:60	0/0:33,0:33:60	0/0:32,0:32:60	0/0:32,0:32:60	0/0:32,0:32:60	0/0:34,0:34:60	0/0:28,0:28:60	0/1:35,22:57:99:500,0,830	0/0:29,0:29:60	0/0:32,0:32:60	0/0:31,0:31:60	0/0:31,0:31:60	0/0:31,0:31:60	0/0:40,0:40:60	0/0:31,0:31:60	0/0:32,0:32:60	0/0:31,0:31:60	0/0:31,0:31:60	0/0:31,0:31:60	0/0:32,0:32:60	0/0:35,0:35:60	0/0:35,0:35:60	0/0:31,0:31:60	0/0:37,0:37:60	0/0:29,0:29:60	0/0:31,0:31:60	0/0:31,0:31:60	0/1:32,35:67:99:770,0,722	0/0:32,0:32:60	0/0:32,0:32:60	0/0:35,0:35:60	0/0:29,0:29:60	0/0:32,0:32:60	0/0:33,0:33:60	0/0:36,0:36:60	0/0:31,0:31:60	0/0:30,0:30:60	0/1:27,19:46:99:413,0,646	0/0:32,0:32:60	0/0:33,0:33:60	0/0:31,0:31:60	0/0:32,0:32:60	0/0:33,0:33:60	0/1:36,25:61:99:520,0,820	0/0:28,0:28:60	0/0:30,0:30:60	0/0:41,0:41:60	0/0:34,0:34:60	0/0:39,0:39:60	0/0:38,0:38:60	0/0:34,0:34:60	0/0:36,0:36:60	0/0:29,0:29:60	0/0:31,0:31:60
+chr1	873542	rs6594027	G	A	360292.25	PASS	AC=123;AF=0.946;AN=130;AS_BaseQRankSum=2.600;AS_FS=0.000;AS_FilterStatus=PASS;AS_InbreedingCoeff=-0.0569;AS_MQ=42.71;AS_MQRankSum=0.850;AS_QD=30.67;AS_ReadPosRankSum=-1.300;AS_SOR=0.875;AS_VQSLOD=0.6987;AS_culprit=AS_MQRankSum;BaseQRankSum=2.68;DB;DP=9543;ExcessHet=0.7388;FS=0.000;InbreedingCoeff=-0.0569;MLEAC=123;MLEAF=0.946;MQ=42.59;MQRankSum=1.08;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=26.61;ReadPosRankSum=-1.219e+00;SOR=0.875	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,304:304:99:.:.:11825,914,0	1/1:0,295:295:99:1|1:873542_G_A:13243,900,0	1/1:0,229:229:99:1|1:873542_G_A:9061,695,0	1/1:0,252:252:99:1|1:873542_G_A:11407,771,0	1/1:0,164:164:99:1|1:873542_G_A:5883,496,0	1/1:0,132:132:99:1|1:873542_G_A:4996,397,0	0/1:39,162:201:99:0|1:873542_G_A:6706,0,1362	1/1:0,128:128:99:.:.:4832,394,0	1/1:0,145:145:99:1|1:873542_G_A:6515,445,0	1/1:0,121:121:99:.:.:4865,370,0	1/1:0,123:123:99:1|1:873542_G_A:4718,373,0	1/1:0,160:160:99:1|1:873542_G_A:7031,485,0	1/1:0,125:125:99:.:.:4931,376,0	0/1:27,128:155:99:.:.:4576,0,306	1/1:0,143:143:99:.:.:5677,433,0	1/1:1,184:185:99:.:.:7035,559,0	1/1:0,161:161:99:1|1:873542_G_A:6171,484,0	0/1:34,163:197:99:0|1:873542_G_A:6640,0,1206	1/1:0,122:122:99:.:.:4878,376,0	1/1:0,134:134:99:1|1:873542_G_A:6156,430,0	1/1:0,131:131:99:1|1:873542_G_A:5024,397,0	1/1:0,135:135:99:.:.:5222,412,0	1/1:1,130:131:99:1|1:873542_G_A:5826,400,0	1/1:0,144:144:99:.:.:5480,436,0	1/1:1,139:140:99:.:.:4523,394,0	1/1:0,118:118:99:.:.:5406,376,0	1/1:0,150:150:99:.:.:5863,460,0	1/1:0,160:160:99:1|1:873542_G_A:7181,491,0	1/1:0,121:121:99:1|1:873542_G_A:4672,367,0	1/1:0,111:111:99:1|1:873542_G_A:5013,346,0	1/1:0,143:143:99:1|1:873542_G_A:6487,445,0	1/1:0,155:155:99:.:.:6278,478,0	1/1:0,146:146:99:.:.:4667,439,0	1/1:0,138:138:99:.:.:4412,414,0	1/1:0,117:117:99:.:.:4646,361,0	0/1:28,169:197:99:0|1:873542_G_A:6911,0,888	1/1:1,138:139:99:.:.:5153,421,0	1/1:2,117:119:99:.:.:3826,352,0	0/1:34,136:170:99:.:.:3848,0,428	1/1:0,106:106:99:.:.:3432,318,0	1/1:0,145:145:99:.:.:4595,436,0	1/1:0,139:139:99:1|1:873542_G_A:6251,427,0	1/1:0,126:126:99:.:.:4231,379,0	1/1:0,135:135:99:.:.:4336,406,0	1/1:0,133:133:99:.:.:4297,400,0	1/1:0,129:129:99:1|1:873542_G_A:4977,394,0	1/1:0,133:133:99:1|1:873542_G_A:5071,403,0	0/1:36,138:174:99:.:.:4024,0,493	1/1:1,117:118:99:.:.:4595,355,0	1/1:0,150:150:99:1|1:873542_G_A:5788,454,0	1/1:0,105:105:99:.:.:4084,322,0	1/1:0,144:144:99:1|1:873542_G_A:5583,436,0	1/1:0,139:139:99:.:.:4531,418,0	1/1:0,128:128:99:.:.:4156,385,0	1/1:0,136:136:99:.:.:5162,424,0	1/1:0,125:125:99:1|1:873542_G_A:5604,385,0	1/1:0,112:112:99:1|1:873542_G_A:4284,343,0	1/1:0,139:139:99:.:.:4576,418,0	1/1:0,105:105:99:1|1:873542_G_A:4696,322,0	1/1:0,97:97:99:.:.:3085,291,0	1/1:1,110:111:99:1|1:873542_G_A:4202,334,0	0/1:47,140:187:99:0|1:873542_G_A:5837,0,1644	1/1:0,136:136:99:.:.:4302,409,0	1/1:0,92:92:99:1|1:873542_G_A:4198,289,0	1/1:0,148:148:99:1|1:873542_G_A:5733,451,0
+chr1	873548	rs11240780	C	T	180143.50	PASS	AC=63;AF=0.485;AN=130;AS_BaseQRankSum=0.000;AS_FS=0.000;AS_FilterStatus=PASS;AS_InbreedingCoeff=-0.0779;AS_MQ=45.20;AS_MQRankSum=0.100;AS_QD=23.59;AS_ReadPosRankSum=-0.200;AS_SOR=0.663;AS_VQSLOD=2.6122;AS_culprit=AS_MQ;BaseQRankSum=0.059;DB;DP=8868;ExcessHet=4.2585;FS=0.000;InbreedingCoeff=-0.0779;MLEAC=63;MLEAF=0.485;MQ=44.97;MQRankSum=0.142;POSITIVE_TRAIN_SITE;QD=23.59;ReadPosRankSum=-1.070e-01;SOR=0.663	GT:AD:DP:GQ:PGT:PID:PL	0/1:155,150:305:99:.:.:4084,0,4165	1/1:0,293:293:99:1|1:873542_G_A:13081,888,0	0/1:115,124:239:99:0|1:873542_G_A:3315,0,3009	1/1:0,259:259:99:1|1:873542_G_A:11566,786,0	0/1:77,86:163:99:0|1:873542_G_A:1719,0,1472	0/1:82,65:147:99:0|1:873542_G_A:1554,0,2136	0/1:38,181:219:99:0|1:873542_G_A:7109,0,1269	0/1:70,66:136:99:.:.:1675,0,1719	1/1:0,150:150:99:1|1:873542_G_A:6630,460,0	0/1:53,78:131:99:.:.:2008,0,1263	0/1:74,57:131:99:0|1:873542_G_A:1524,0,1882	1/1:0,152:152:99:1|1:873542_G_A:6839,467,0	0/1:59,70:129:99:.:.:1778,0,1540	0/1:84,74:158:99:.:.:1734,0,2852	0/1:67,85:152:99:.:.:2241,0,1738	0/1:105,92:197:99:.:.:2277,0,2734	0/1:76,84:160:99:0|1:873542_G_A:2155,0,1890	0/1:33,161:194:99:0|1:873542_G_A:6630,0,1185	0/1:58,72:130:99:.:.:1878,0,1508	1/1:0,138:138:99:1|1:873542_G_A:6127,427,0	0/1:69,61:130:99:0|1:873542_G_A:1516,0,1871	0/1:75,68:143:99:.:.:1703,0,1938	1/1:1,139:140:99:1|1:873542_G_A:6079,424,0	0/1:83,70:153:99:.:.:1765,0,2124	0/0:35,0:35:60	1/1:2,124:126:99:.:.:3889,350,0	0/1:76,80:156:99:.:.:2000,0,1996	1/1:0,162:162:99:1|1:873542_G_A:7230,497,0	0/1:64,62:126:99:0|1:873542_G_A:1656,0,1549	1/1:0,109:109:99:1|1:873542_G_A:4850,334,0	1/1:0,152:152:99:1|1:873542_G_A:6644,463,0	0/1:64,99:163:99:.:.:2656,0,1546	0/0:156,0:156:60	0/0:144,0:144:60	0/1:69,62:131:99:.:.:1645,0,1828	0/1:26,165:191:99:0|1:873542_G_A:6858,0,847	0/1:87,58:145:99:.:.:1424,0,2266	0/0:107,0:107:60	0/0:62,0:62:60	0/0:38,0:38:60	0/0:37,0:37:60	1/1:0,143:143:99:1|1:873542_G_A:6398,442,0	0/0:142,0:142:60	0/0:37,0:37:60	0/0:38,0:38:60	0/1:72,71:143:99:0|1:873542_G_A:1789,0,1854	0/1:73,64:137:99:0|1:873542_G_A:1596,0,1873	0/0:79,0:79:60	0/1:54,69:123:99:.:.:1810,0,1357	0/1:76,79:155:99:0|1:873542_G_A:1987,0,2008	0/1:52,56:108:99:.:.:1434,0,1365	0/1:70,79:149:99:0|1:873542_G_A:2086,0,1760	0/0:35,0:35:60	0/0:36,0:36:60	0/1:77,63:140:99:.:.:1583,0,1930	1/1:0,129:129:99:1|1:873542_G_A:5699,394,0	0/1:68,52:120:99:0|1:873542_G_A:1295,0,1790	0/0:123,0:123:60	1/1:0,105:105:99:1|1:873542_G_A:4740,325,0	0/0:41,0:41:60	0/1:64,57:121:99:0|1:873542_G_A:1422,0,1602	0/1:45,156:201:99:0|1:873542_G_A:6061,0,1556	0/0:107,0:107:60	1/1:0,96:96:99:1|1:873542_G_A:4197,289,0	0/1:75,81:156:99:0|1:873542_G_A:2157,0,1887
+chr1	873857	rs200657693	C	G	874.77	PASS	AC=7;AF=0.054;AN=130;AS_BaseQRankSum=0.000;AS_FS=0.851;AS_FilterStatus=PASS;AS_InbreedingCoeff=-0.0550;AS_MQ=24.53;AS_MQRankSum=-3.900;AS_QD=0.94;AS_ReadPosRankSum=-0.100;AS_SOR=0.828;AS_VQSLOD=-5.1802;AS_culprit=AS_MQ;BaseQRankSum=0.079;DB;DP=4413;ExcessHet=0.7388;FS=0.851;InbreedingCoeff=-0.0550;MLEAC=6;MLEAF=0.046;MQ=33.43;MQRankSum=-3.895e+00;QD=0.94;ReadPosRankSum=-4.400e-02;SOR=0.828	GT:AD:DP:GQ:PL	0/0:37,0:37:60	0/0:36,0:36:60	0/0:32,0:32:60	0/0:31,0:31:60	0/0:119,0:119:60	0/0:34,0:34:60	0/0:99,0:99:60	0/0:37,0:37:60	0/1:115,19:134:99:149,0,3175	0/0:34,0:34:60	0/0:137,0:137:60	0/0:35,0:35:60	0/1:104,15:119:17:17,0,2931	0/0:41,0:41:60	0/0:41,0:41:60	0/0:35,0:35:60	0/0:37,0:37:60	0/0:61,0:61:60	0/0:38,0:38:60	0/0:145,0:145:60	0/0:114,0:114:60	0/1:107,22:129:99:182,0,2959	0/0:32,0:32:60	0/0:36,0:36:60	0/0:35,0:35:60	0/0:37,0:37:60	0/0:75,0:75:60	0/1:105,26:131:99:312,0,2985	0/0:110,0:110:60	0/0:32,0:32:60	0/0:37,0:37:60	0/0:36,0:36:60	0/0:156,0:156:60	0/0:144,0:144:60	0/0:43,0:43:60	0/0:40,0:40:60	0/0:42,0:42:60	0/0:41,0:41:60	0/0:62,0:62:60	0/0:38,0:38:60	0/0:37,0:37:60	0/0:36,0:36:60	0/0:132,0:132:60	0/0:37,0:37:60	0/0:38,0:38:60	0/0:109,0:109:60	0/0:89,0:89:60	0/0:37,0:37:60	0/0:118,0:118:60	0/0:40,0:40:60	0/0:45,0:45:60	0/0:37,0:37:60	0/0:35,0:35:60	0/0:36,0:36:60	0/0:34,0:34:60	0/1:107,20:127:99:189,0,2965	0/0:39,0:39:60	0/1:153,20:173:6:6,0,4170	0/0:34,0:34:60	0/0:41,0:41:60	0/1:101,16:117:86:86,0,2791	0/0:83,0:83:60	0/0:107,0:107:60	0/0:42,0:42:60	0/0:138,0:138:60
+chr1	873921	.	C	T	316.29	VQSRTrancheSNP99.00to99.90+	AC=3;AF=0.023;AN=130;AS_BaseQRankSum=1.300;AS_FS=52.348;AS_FilterStatus=VQSRTrancheSNP99.00to99.90+;AS_InbreedingCoeff=-0.0237;AS_MQ=33.06;AS_MQRankSum=-1.800;AS_QD=0.70;AS_ReadPosRankSum=0.700;AS_SOR=7.505;AS_VQSLOD=-31.6520;AS_culprit=AS_FS;BaseQRankSum=1.37;DP=3803;ExcessHet=0.1022;FS=52.348;InbreedingCoeff=-0.0237;MLEAC=3;MLEAF=0.023;MQ=35.04;MQRankSum=-1.751e+00;QD=0.70;ReadPosRankSum=0.784;SOR=7.505	GT:AD:DP:GQ:PL	0/0:37,0:37:60	0/0:36,0:36:60	0/0:32,0:32:60	0/0:31,0:31:60	0/0:68,0:68:60	0/0:34,0:34:60	0/0:99,0:99:60	0/0:37,0:37:60	0/1:150,20:170:99:134,0,4252	0/0:34,0:34:60	0/0:33,0:33:60	0/0:35,0:35:60	0/0:38,0:38:60	0/0:41,0:41:60	0/0:41,0:41:60	0/0:35,0:35:60	0/0:37,0:37:60	0/0:61,0:61:60	0/0:38,0:38:60	0/0:145,0:145:60	0/0:137,0:137:20	0/0:34,0:34:60	0/0:32,0:32:60	0/0:36,0:36:60	0/0:35,0:35:60	0/0:37,0:37:60	0/0:75,0:75:60	0/0:37,0:37:60	0/1:126,18:144:84:84,0,3713	0/0:32,0:32:60	0/0:37,0:37:60	0/0:36,0:36:60	0/0:156,0:156:60	0/0:144,0:144:60	0/0:43,0:43:60	0/0:40,0:40:60	0/0:42,0:42:60	0/0:41,0:41:60	0/0:62,0:62:60	0/0:38,0:38:60	0/0:37,0:37:60	0/0:36,0:36:60	0/0:132,0:132:60	0/0:37,0:37:60	0/0:38,0:38:60	0/1:120,17:137:99:139,0,3406	0/0:89,0:89:60	0/0:37,0:37:60	0/0:118,0:118:60	0/0:40,0:40:60	0/0:45,0:45:60	0/0:37,0:37:60	0/0:35,0:35:60	0/0:36,0:36:60	0/0:34,0:34:60	0/0:37,0:37:60	0/0:39,0:39:60	0/0:38,0:38:60	0/0:34,0:34:60	0/0:41,0:41:60	0/0:35,0:35:60	0/0:83,0:83:60	0/0:107,0:107:60	0/0:42,0:42:60	0/0:138,0:138:60
+chr1	874460	.	C	A	804.62	PASS	AC=1;AF=7.692e-03;AN=130;AS_BaseQRankSum=0.000;AS_FS=0.000;AS_FilterStatus=PASS;AS_InbreedingCoeff=-0.0078;AS_MQ=60.00;AS_MQRankSum=0.000;AS_QD=16.10;AS_ReadPosRankSum=1.500;AS_SOR=0.952;AS_VQSLOD=8.2162;AS_culprit=AS_MQ;BaseQRankSum=0.00;DP=2844;ExcessHet=0.0000;FS=0.000;InbreedingCoeff=-0.0078;MLEAC=1;MLEAF=7.692e-03;MQ=60.00;MQRankSum=0.00;QD=16.09;ReadPosRankSum=1.60;SOR=0.952	GT:AD:DP:GQ:PL	0/0:37,0:37:60	0/0:36,0:36:60	0/0:32,0:32:60	0/0:31,0:31:60	0/0:68,0:68:60	0/0:34,0:34:60	0/0:99,0:99:60	0/0:37,0:37:60	0/0:170,0:170:60	0/0:34,0:34:60	0/0:33,0:33:60	0/0:35,0:35:60	0/0:38,0:38:60	0/0:41,0:41:60	0/0:41,0:41:60	0/0:35,0:35:60	0/0:37,0:37:60	0/0:61,0:61:60	0/0:38,0:38:60	0/0:35,0:35:60	0/0:35,0:35:60	0/0:34,0:34:60	0/0:32,0:32:60	0/0:36,0:36:60	0/0:35,0:35:60	0/0:37,0:37:60	0/0:75,0:75:60	0/0:37,0:37:60	0/0:34,0:34:60	0/0:32,0:32:60	0/0:37,0:37:60	0/0:36,0:36:60	0/0:156,0:156:60	0/1:22,28:50:99:823,0,614	0/0:43,0:43:60	0/0:40,0:40:60	0/0:42,0:42:60	0/0:41,0:41:60	0/0:62,0:62:60	0/0:38,0:38:60	0/0:37,0:37:60	0/0:36,0:36:60	0/0:34,0:34:60	0/0:37,0:37:60	0/0:38,0:38:60	0/0:41,0:41:60	0/0:89,0:89:60	0/0:37,0:37:60	0/0:35,0:35:60	0/0:40,0:40:60	0/0:45,0:45:60	0/0:37,0:37:60	0/0:35,0:35:60	0/0:36,0:36:60	0/0:34,0:34:60	0/0:37,0:37:60	0/0:39,0:39:60	0/0:38,0:38:60	0/0:34,0:34:60	0/0:41,0:41:60	0/0:35,0:35:60	0/0:23,0:23:60	0/0:31,0:31:50	0/0:16,0:16:30	0/0:35,0:35:60
+chr1	930939	rs9988021	G	A	67117.32	PASS	AC=129;AF=0.992;AN=130;AS_BaseQRankSum=0.500;AS_FS=0.000;AS_FilterStatus=PASS;AS_InbreedingCoeff=-0.0078;AS_MQ=60.00;AS_MQRankSum=0.000;AS_QD=34.24;AS_ReadPosRankSum=0.800;AS_SOR=6.051;AS_VQSLOD=8.8136;AS_culprit=AS_MQ;BaseQRankSum=0.501;DB;DP=1968;ExcessHet=0.0000;FS=0.000;InbreedingCoeff=-0.0078;MLEAC=129;MLEAF=0.992;MQ=60.00;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=34.24;ReadPosRankSum=0.843;SOR=6.051	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,56:56:99:.:.:1870,168,0	1/1:0,42:42:99:.:.:1419,126,0	1/1:0,42:42:99:.:.:1400,126,0	1/1:0,48:48:99:.:.:1528,144,0	0/1:18,17:35:99:.:.:406,0,380	1/1:0,29:29:87:.:.:1007,87,0	1/1:0,30:30:90:.:.:986,90,0	1/1:0,31:31:93:.:.:1037,93,0	1/1:0,23:23:69:.:.:798,69,0	1/1:0,21:21:63:.:.:730,63,0	1/1:0,37:37:99:.:.:1251,111,0	1/1:0,23:23:69:.:.:777,69,0	1/1:0,16:16:48:.:.:546,48,0	1/1:0,32:32:96:.:.:1101,96,0	1/1:0,43:43:99:.:.:1474,129,0	1/1:0,35:35:99:.:.:1184,105,0	1/1:0,30:30:90:.:.:1021,90,0	1/1:0,28:28:84:.:.:973,84,0	1/1:0,25:25:75:.:.:848,75,0	1/1:0,35:35:99:.:.:1161,105,0	1/1:0,38:38:99:.:.:1259,113,0	1/1:0,25:25:75:.:.:849,75,0	1/1:0,27:27:81:.:.:898,81,0	1/1:0,28:28:84:.:.:973,84,0	1/1:0,39:39:99:.:.:1326,117,0	1/1:0,28:28:84:.:.:942,84,0	1/1:0,33:33:99:.:.:1145,99,0	1/1:0,32:32:96:.:.:1082,96,0	1/1:0,33:33:99:.:.:1087,99,0	1/1:0,33:33:99:.:.:1137,99,0	1/1:0,29:29:87:.:.:1008,87,0	1/1:0,17:17:51:.:.:580,51,0	1/1:0,20:20:60:.:.:674,60,0	1/1:0,32:32:96:.:.:1065,96,0	1/1:0,25:25:75:.:.:857,75,0	1/1:0,32:32:96:.:.:1071,96,0	1/1:0,23:23:69:.:.:788,69,0	1/1:0,23:23:69:.:.:769,69,0	1/1:0,43:43:99:.:.:1485,129,0	1/1:0,25:25:75:.:.:844,75,0	1/1:0,28:28:84:.:.:926,84,0	1/1:0,28:28:84:.:.:948,84,0	1/1:0,33:33:99:.:.:1145,99,0	1/1:0,43:43:99:.:.:1453,129,0	1/1:0,20:20:60:.:.:694,60,0	1/1:0,30:30:90:.:.:1002,90,0	1/1:0,38:38:99:.:.:1320,114,0	1/1:0,29:29:87:.:.:1006,87,0	1/1:0,17:17:51:.:.:590,51,0	1/1:0,31:31:93:.:.:1056,93,0	1/1:0,29:29:87:.:.:1006,87,0	1/1:0,36:36:99:.:.:1220,108,0	1/1:0,23:23:69:.:.:767,69,0	1/1:0,31:31:93:.:.:1057,93,0	1/1:0,31:31:93:.:.:1051,93,0	1/1:0,25:25:75:.:.:844,75,0	1/1:0,20:20:60:.:.:685,60,0	1/1:0,35:35:99:.:.:1170,105,0	1/1:0,27:27:81:.:.:929,81,0	1/1:0,28:28:84:.:.:973,84,0	1/1:0,29:29:87:.:.:988,87,0	1/1:0,26:26:78:1|1:930937_G_A:903,78,0	1/1:0,32:32:96:.:.:1092,96,0	1/1:0,25:25:75:.:.:859,75,0	1/1:0,20:20:60:.:.:695,60,0
+chr1	931131	rs60722469	C	CCCCT	37940.21	VQSRTrancheINDEL95.00to96.00	AC=79;AF=0.608;AN=130;AS_BaseQRankSum=-0.200;AS_FS=19.073;AS_FilterStatus=VQSRTrancheINDEL95.00to96.00;AS_InbreedingCoeff=-0.0052;AS_MQ=60.00;AS_MQRankSum=0.000;AS_QD=29.01;AS_ReadPosRankSum=-0.500;AS_SOR=2.445;AS_VQSLOD=-0.4942;AS_culprit=AS_FS;BaseQRankSum=-1.570e-01;DB;DP=2563;ExcessHet=2.0236;FS=19.073;InbreedingCoeff=-0.0052;MLEAC=78;MLEAF=0.600;MQ=59.99;MQRankSum=0.00;QD=29.01;ReadPosRankSum=-4.610e-01;SOR=2.423	GT:AD:DP:GQ:PGT:PID:PL	0/0:77,0:77:60	0/1:32,42:74:99:.:.:1059,0,906	0/1:13,49:62:99:0|1:931131_C_CCCCT:2016,0,224	0/1:15,32:47:99:0|1:931131_C_CCCCT:1367,0,378	0/1:14,8:22:99:.:.:293,0,698	1/1:0,18:18:52:.:.:706,52,0	0/0:34,0:34:60	0/0:36,0:36:60	0/1:7,15:22:99:.:.:698,0,285	1/1:0,21:21:62:.:.:890,62,0	0/1:18,11:29:99:.:.:358,0,893	0/1:8,6:14:99:.:.:201,0,424	0/1:6,9:15:99:.:.:319,0,282	0/1:18,13:31:99:.:.:501,0,836	1/1:0,23:23:68:.:.:970,68,0	0/1:17,11:28:99:.:.:398,0,699	1/1:0,19:19:57:.:.:843,57,0	0/1:7,13:20:99:.:.:492,0,245	0/0:34,0:34:60	0/1:8,8:16:99:.:.:306,0,370	1/1:1,12:13:10:.:.:510,10,0	0/1:6,10:16:99:.:.:471,0,249	0/1:12,8:20:99:.:.:315,0,591	0/1:7,9:16:99:.:.:345,0,358	1/1:0,32:32:98:.:.:1418,98,0	0/0:32,0:32:60	1/1:0,26:26:80:.:.:1171,80,0	1/1:0,30:30:95:.:.:1345,95,0	0/1:8,15:23:99:.:.:587,0,348	0/1:1,18:19:2:.:.:679,0,2	1/1:1,20:21:7:.:.:863,7,0	1/1:0,15:15:44:.:.:663,44,0	1/1:0,22:22:71:.:.:1046,71,0	0/0:47,0:47:60	0/1:9,7:16:99:.:.:249,0,398	0/1:13,12:25:99:.:.:426,0,650	0/1:18,11:29:99:.:.:443,0,687	1/1:1,18:19:11:.:.:720,11,0	0/1:17,15:32:99:.:.:496,0,796	0/1:8,12:20:99:.:.:447,0,307	1/1:1,15:16:22:.:.:697,22,0	0/1:10,7:17:99:.:.:252,0,505	1/1:0,25:25:80:.:.:1076,80,0	1/1:0,23:23:68:.:.:980,68,0	1/1:0,22:22:71:.:.:1024,71,0	1/1:0,12:12:38:.:.:536,38,0	0/1:18,12:30:99:.:.:468,0,672	0/0:43,0:43:60	0/0:32,0:32:60	1/1:1,29:30:47:.:.:1167,47,0	1/1:1,15:16:5:.:.:663,5,0	1/1:0,19:19:56:.:.:837,56,0	0/1:6,14:20:99:.:.:574,0,186	0/1:14,12:26:99:.:.:440,0,601	1/1:0,29:29:86:.:.:1247,86,0	0/1:12,5:17:99:.:.:201,0,646	1/1:1,21:22:23:.:.:788,23,0	0/1:12,11:23:99:.:.:436,0,487	0/0:37,0:37:60	0/0:35,0:35:60	1/1:0,13:13:38:.:.:552,38,0	0/1:8,15:23:99:.:.:559,0,290	0/1:11,9:22:99:.:.:281,0,582	1/1:0,23:23:74:.:.:1027,74,0	0/1:18,9:27:99:.:.:342,0,896
+chr1	931143	.	T	C	1125.29	VQSRTrancheSNP99.00to99.90+	AC=3;AF=0.023;AN=130;AS_BaseQRankSum=-2.700;AS_FS=342.391;AS_FilterStatus=VQSRTrancheSNP99.00to99.90+;AS_InbreedingCoeff=-0.0237;AS_MQ=59.70;AS_MQRankSum=0.000;AS_QD=5.18;AS_ReadPosRankSum=1.200;AS_SOR=8.051;AS_VQSLOD=-725.0645;AS_culprit=AS_FS;BaseQRankSum=-2.622e+00;DP=2198;ExcessHet=0.1022;FS=342.391;InbreedingCoeff=-0.0237;MLEAC=3;MLEAF=0.023;MQ=59.92;MQRankSum=0.00;QD=5.19;ReadPosRankSum=1.30;SOR=8.051	GT:AD:DP:GQ:PGT:PID:PL	0/0:77,0:77:60	0/1:53,30:83:99:0|1:931143_T_C:742,0,2079	0/1:63,11:74:99:0|1:931143_T_C:116,0,2575	0/1:46,14:60:99:0|1:931143_T_C:308,0,1791	0/0:30,0:30:40	0/0:27,0:27:30	0/0:29,0:29:50	0/0:36,0:36:60	0/0:41,0:41:60	0/0:35,0:35:60	0/0:36,0:36:60	0/0:23,0:23:50	0/0:21,0:21:40	0/0:44,0:44:60	0/0:27,0:27:40	0/0:35,0:35:60	0/0:26,0:26:50	0/0:29,0:29:40	0/0:27,0:27:60	0/0:26,0:26:60	0/0:19,0:19:20	0/0:20,0:20:30	0/0:37,0:37:60	0/0:22,0:22:50	0/0:38,0:38:60	0/0:32,0:32:60	0/0:31,0:31:60	0/0:41,0:41:60	0/0:32,0:32:60	0/0:26,0:26:40	0/0:28,0:28:50	0/0:22,0:22:40	0/0:36,0:36:60	0/0:36,0:36:50	0/0:20,0:20:30	0/0:38,0:38:60	0/0:49,0:49:60	0/0:29,0:29:40	0/0:44,0:44:60	0/0:30,0:30:50	0/0:23,0:23:40	0/0:28,0:28:50	0/0:34,0:34:60	0/0:31,0:31:60	0/0:29,0:29:60	0/0:20,0:20:40	0/0:39,0:39:60	0/0:43,0:43:60	0/0:32,0:32:60	0/0:34,0:34:60	0/0:25,0:25:40	0/0:25,0:25:50	0/0:23,0:23:50	0/0:33,0:33:60	0/0:37,0:37:50	0/0:24,0:24:50	0/0:34,0:34:50	0/0:41,0:41:60	0/0:37,0:37:60	0/0:35,0:35:60	0/0:23,0:23:30	0/0:36,0:36:50	0/0:27,0:27:50	0/0:32,0:32:50	0/0:35,0:35:60
+chr1	935662	rs199537431	C	CA	1154.59	PASS	AC=1;AF=7.692e-03;AN=130;AS_BaseQRankSum=-0.900;AS_FS=0.000;AS_FilterStatus=PASS;AS_InbreedingCoeff=-0.0078;AS_MQ=60.00;AS_MQRankSum=0.000;AS_QD=18.33;AS_ReadPosRankSum=0.700;AS_SOR=0.933;AS_VQSLOD=3.8398;AS_culprit=AS_QD;BaseQRankSum=-8.390e-01;DB;DP=3105;ExcessHet=0.0000;FS=0.000;InbreedingCoeff=-0.0078;MLEAC=1;MLEAF=7.692e-03;MQ=60.00;MQRankSum=0.00;QD=18.33;ReadPosRankSum=0.895;SOR=1.000	GT:AD:DP:GQ:PL	0/0:71,0:71:60	0/0:29,0:29:60	0/0:29,0:29:60	0/0:22,0:22:50	0/0:32,0:32:60	0/0:36,0:36:60	0/0:39,0:39:60	0/0:37,0:37:60	0/0:41,0:41:60	0/0:38,0:38:60	0/0:38,0:38:60	0/0:50,0:50:60	0/0:34,0:34:60	0/0:38,0:38:60	0/0:41,0:41:60	0/0:51,0:51:60	0/0:39,0:39:60	0/0:40,0:40:60	0/0:189,0:189:60	0/0:38,0:38:60	0/0:37,0:37:60	0/0:38,0:38:60	0/0:43,0:43:60	0/0:45,0:45:60	0/0:45,0:45:60	0/0:45,0:45:60	0/0:36,0:36:60	0/0:45,0:45:60	0/0:40,0:40:60	0/0:36,0:36:60	0/0:53,0:53:60	0/0:50,0:50:60	0/0:40,0:40:60	0/0:47,0:47:60	0/1:28,35:65:99:1173,0,847	0/0:39,0:39:60	0/0:38,0:38:60	0/0:42,0:42:60	0/0:36,0:36:60	0/0:32,0:32:60	0/0:49,0:49:60	0/0:38,0:38:60	0/0:38,0:38:60	0/0:43,0:43:60	0/0:42,0:42:60	0/0:46,0:46:60	0/0:35,0:35:60	0/0:40,0:40:60	0/0:162,0:162:60	0/0:36,0:36:60	0/0:40,0:40:60	0/0:49,0:49:60	0/0:127,0:127:60	0/0:40,0:40:60	0/0:44,0:44:60	0/0:36,0:36:60	0/0:34,0:34:60	0/0:167,0:167:60	0/0:33,0:33:60	0/0:37,0:37:60	0/0:42,0:42:60	0/0:33,0:33:60	0/0:35,0:35:60	0/0:30,0:30:60	0/0:43,0:43:60
+chr1	935835	rs28419423	C	G	6303.83	PASS	AC=4;AF=0.031;AN=130;AS_BaseQRankSum=0.350;AS_FS=0.989;AS_FilterStatus=PASS;AS_InbreedingCoeff=-0.0317;AS_MQ=60.00;AS_MQRankSum=0.000;AS_QD=14.69;AS_ReadPosRankSum=0.650;AS_SOR=0.888;AS_VQSLOD=7.5347;AS_culprit=AS_MQ;BaseQRankSum=1.33;DB;DP=2885;ExcessHet=0.2060;FS=0.989;InbreedingCoeff=-0.0317;MLEAC=4;MLEAF=0.031;MQ=59.99;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=14.69;ReadPosRankSum=0.709;SOR=0.888	GT:AD:DP:GQ:PL	0/0:71,0:71:60	0/0:29,0:29:60	0/0:29,0:29:60	0/0:39,0:39:60	0/0:32,0:32:60	0/0:36,0:36:60	0/0:39,0:39:60	0/0:37,0:37:60	0/0:41,0:41:60	0/0:38,0:38:60	0/0:38,0:38:60	0/0:50,0:50:60	0/0:34,0:34:60	0/0:38,0:38:60	0/0:41,0:41:60	0/0:51,0:51:60	0/0:39,0:39:60	0/0:40,0:40:60	0/1:54,68:122:99:1802,0,1414	0/0:38,0:38:60	0/0:37,0:37:60	0/0:38,0:38:60	0/0:43,0:43:60	0/0:45,0:45:60	0/0:45,0:45:60	0/0:45,0:45:60	0/0:36,0:36:60	0/0:45,0:45:60	0/0:40,0:40:60	0/0:36,0:36:60	0/0:53,0:53:60	0/0:50,0:50:60	0/0:40,0:40:60	0/0:47,0:47:60	0/0:46,0:46:60	0/0:39,0:39:60	0/0:38,0:38:60	0/0:42,0:42:60	0/0:36,0:36:60	0/0:32,0:32:60	0/0:49,0:49:60	0/0:38,0:38:60	0/0:38,0:38:60	0/0:43,0:43:60	0/0:42,0:42:60	0/0:46,0:46:60	0/0:35,0:35:60	0/0:40,0:40:60	0/1:51,55:106:99:1512,0,1347	0/0:36,0:36:60	0/0:40,0:40:60	0/0:49,0:49:60	0/1:50,43:93:99:1189,0,1254	0/0:40,0:40:60	0/0:44,0:44:60	0/0:36,0:36:60	0/0:34,0:34:60	0/1:42,66:108:99:1850,0,1097	0/0:33,0:33:60	0/0:37,0:37:60	0/0:42,0:42:60	0/0:33,0:33:60	0/0:35,0:35:60	0/0:30,0:30:60	0/0:43,0:43:60
+chr1	939334	rs201596485	C	T	148.62	PASS	AC=1;AF=7.692e-03;AN=130;AS_BaseQRankSum=-1.400;AS_FS=0.000;AS_FilterStatus=PASS;AS_InbreedingCoeff=-0.0078;AS_MQ=60.00;AS_MQRankSum=0.000;AS_QD=6.77;AS_ReadPosRankSum=1.000;AS_SOR=0.446;AS_VQSLOD=8.9570;AS_culprit=AS_MQ;BaseQRankSum=-1.366e+00;DB;DP=2020;ExcessHet=0.0000;FS=0.000;InbreedingCoeff=-0.0078;MLEAC=1;MLEAF=7.692e-03;MQ=60.00;MQRankSum=0.00;QD=6.76;ReadPosRankSum=1.06;SOR=0.446	GT:AD:DP:GQ:PL	0/0:40,0:40:60	0/0:39,0:39:60	0/0:34,0:34:60	0/0:33,0:33:60	0/0:30,0:30:60	0/0:32,0:32:60	0/0:38,0:38:60	0/0:30,0:30:60	0/0:26,0:26:60	0/0:37,0:37:60	0/1:15,7:22:99:167,0,455	0/0:33,0:33:60	0/0:33,0:33:60	0/0:27,0:27:60	0/0:31,0:31:60	0/0:37,0:37:60	0/0:23,0:23:50	0/0:31,0:31:60	0/0:30,0:30:60	0/0:33,0:33:60	0/0:32,0:32:60	0/0:27,0:27:60	0/0:34,0:34:60	0/0:33,0:33:60	0/0:25,0:25:60	0/0:29,0:29:60	0/0:33,0:33:60	0/0:32,0:32:60	0/0:29,0:29:60	0/0:32,0:32:60	0/0:24,0:24:60	0/0:37,0:37:60	0/0:33,0:33:60	0/0:23,0:23:50	0/0:35,0:35:60	0/0:32,0:32:60	0/0:26,0:26:60	0/0:22,0:22:50	0/0:35,0:35:60	0/0:25,0:25:50	0/0:33,0:33:60	0/0:32,0:32:60	0/0:36,0:36:60	0/0:23,0:23:30	0/0:32,0:32:60	0/0:22,0:22:50	0/0:36,0:36:60	0/0:30,0:30:60	0/0:29,0:29:60	0/0:31,0:31:60	0/0:32,0:32:60	0/0:31,0:31:60	0/0:33,0:33:60	0/0:29,0:29:60	0/0:35,0:35:60	0/0:36,0:36:60	0/0:37,0:37:60	0/0:33,0:33:60	0/0:33,0:33:60	0/0:32,0:32:60	0/0:29,0:29:60	0/0:30,0:30:60	0/0:32,0:32:60	0/0:27,0:27:60	0/0:30,0:30:60
+chr1	939354	rs145967298	C	T	2198.83	PASS	AC=4;AF=0.031;AN=130;AS_BaseQRankSum=-0.400;AS_FS=1.470;AS_FilterStatus=PASS;AS_InbreedingCoeff=-0.0317;AS_MQ=60.00;AS_MQRankSum=0.000;AS_QD=14.96;AS_ReadPosRankSum=1.100;AS_SOR=0.864;AS_VQSLOD=6.9303;AS_culprit=AS_MQ;BaseQRankSum=-8.200e-02;DB;DP=2144;ExcessHet=0.2060;FS=1.470;InbreedingCoeff=-0.0317;MLEAC=4;MLEAF=0.031;MQ=60.00;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=14.96;ReadPosRankSum=1.62;SOR=0.864	GT:AD:DP:GQ:PL	0/0:40,0:40:60	0/0:39,0:39:60	0/0:34,0:34:60	0/0:33,0:33:60	0/0:30,0:30:60	0/0:32,0:32:60	0/0:38,0:38:60	0/0:30,0:30:60	0/0:26,0:26:60	0/0:37,0:37:60	0/0:26,0:26:60	0/0:33,0:33:60	0/0:33,0:33:60	0/0:27,0:27:60	0/0:31,0:31:60	0/0:37,0:37:60	0/0:33,0:33:60	0/0:31,0:31:60	0/0:30,0:30:60	0/0:33,0:33:60	0/0:32,0:32:60	0/0:27,0:27:60	0/0:34,0:34:60	0/0:33,0:33:60	0/0:36,0:36:60	0/0:29,0:29:60	0/0:33,0:33:60	0/1:21,22:43:99:551,0,581	0/0:29,0:29:60	0/0:32,0:32:60	0/0:21,0:21:50	0/0:37,0:37:60	0/0:33,0:33:60	0/0:39,0:39:60	0/0:35,0:35:60	0/1:13,17:30:99:491,0,337	0/0:37,0:37:60	0/0:32,0:32:60	0/0:35,0:35:60	0/0:27,0:27:40	0/0:33,0:33:60	0/0:32,0:32:60	0/0:36,0:36:60	0/0:33,0:33:60	0/0:40,0:40:60	0/0:35,0:35:60	0/0:36,0:36:60	0/0:31,0:31:60	0/0:29,0:29:60	0/0:31,0:31:60	0/0:32,0:32:60	0/0:35,0:35:60	0/0:33,0:33:60	0/0:29,0:29:60	0/0:35,0:35:60	0/0:36,0:36:60	0/1:18,22:40:99:584,0,460	0/0:33,0:33:60	0/0:33,0:33:60	0/0:32,0:32:60	0/1:12,22:34:99:622,0,295	0/0:30,0:30:60	0/0:32,0:32:60	0/0:34,0:34:60	0/0:30,0:30:60
+chr1	939484	rs141512630	CT	C	176.59	VQSRTrancheINDEL95.00to96.00	AC=1;AF=7.692e-03;AN=130;AS_BaseQRankSum=0.500;AS_FS=3.402;AS_FilterStatus=VQSRTrancheINDEL95.00to96.00;AS_InbreedingCoeff=-0.0078;AS_MQ=58.47;AS_MQRankSum=-1.700;AS_QD=4.02;AS_ReadPosRankSum=-1.500;AS_SOR=0.268;AS_VQSLOD=-0.6931;AS_culprit=AS_QD;BaseQRankSum=0.501;DB;DP=2255;ExcessHet=0.0000;FS=3.402;InbreedingCoeff=-0.0078;MLEAC=1;MLEAF=7.692e-03;MQ=59.62;MQRankSum=-1.680e+00;QD=4.01;ReadPosRankSum=-1.425e+00;SOR=0.268	GT:AD:DP:GQ:PL	0/0:40,0:40:60	0/0:39,0:39:60	0/0:34,0:34:60	0/0:33,0:33:60	0/0:93,0:93:60	0/0:32,0:32:60	0/0:38,0:38:60	0/0:30,0:30:60	0/0:37,0:37:60	0/0:37,0:37:60	0/0:26,0:26:60	0/0:33,0:33:60	0/0:33,0:33:60	0/0:27,0:27:60	0/0:31,0:31:60	0/0:37,0:37:60	0/0:33,0:33:60	0/0:31,0:31:60	0/0:30,0:30:60	0/0:32,0:32:50	0/0:42,0:42:60	0/0:35,0:35:60	0/0:34,0:34:60	0/0:33,0:33:60	0/0:38,0:38:60	0/0:29,0:29:60	0/0:46,0:46:60	0/0:42,0:42:60	0/0:29,0:29:60	0/0:26,0:26:50	0/0:31,0:31:60	0/0:42,0:42:60	0/0:33,0:33:60	0/0:39,0:39:60	0/0:33,0:33:60	0/0:36,0:36:60	0/0:37,0:37:60	0/0:32,0:32:60	0/0:35,0:35:60	0/0:33,0:33:60	0/0:33,0:33:60	0/0:32,0:32:60	0/0:25,0:25:60	0/0:33,0:33:60	0/0:40,0:40:60	0/0:21,0:21:60	0/0:29,0:29:60	0/0:31,0:31:60	0/0:29,0:29:60	0/1:33,11:44:99:195,0,1063	0/0:32,0:32:60	0/0:35,0:35:60	0/0:33,0:33:60	0/0:29,0:29:60	0/0:41,0:41:60	0/0:36,0:36:60	0/0:39,0:39:60	0/0:33,0:33:60	0/0:33,0:33:60	0/0:32,0:32:60	0/0:38,0:38:60	0/0:30,0:30:60	0/0:32,0:32:60	0/0:34,0:34:60	0/0:30,0:30:60
+chr1	943045	.	C	T	414.32	PASS	AC=2;AF=0.015;AN=130;AS_BaseQRankSum=-0.150;AS_FS=1.189;AS_FilterStatus=PASS;AS_InbreedingCoeff=-0.0165;AS_MQ=60.00;AS_MQRankSum=0.000;AS_QD=9.20;AS_ReadPosRankSum=0.900;AS_SOR=0.410;AS_VQSLOD=5.3112;AS_culprit=AS_MQ;BaseQRankSum=0.717;DP=1439;ExcessHet=0.0338;FS=1.189;InbreedingCoeff=-0.0166;MLEAC=2;MLEAF=0.015;MQ=60.00;MQRankSum=0.00;QD=9.21;ReadPosRankSum=1.37;SOR=0.410	GT:AD:DP:GQ:PL	0/0:18,0:18:50	0/0:12,0:12:30	0/0:13,0:13:30	0/0:8,0:8:20	0/0:28,0:28:60	0/0:23,0:23:50	0/0:29,0:29:60	0/0:26,0:26:60	0/0:13,0:13:30	0/0:24,0:24:60	0/0:21,0:21:50	0/0:25,0:25:60	0/0:13,0:13:30	0/0:27,0:27:60	0/0:19,0:19:50	0/0:29,0:29:60	0/1:11,9:20:99:233,0,282	0/0:32,0:32:60	0/0:24,0:24:40	0/0:26,0:26:60	0/0:17,0:17:50	0/0:18,0:18:50	0/0:28,0:28:60	0/0:31,0:31:60	0/0:22,0:22:60	0/0:24,0:24:60	0/0:15,0:15:30	0/0:26,0:26:60	0/0:19,0:19:50	0/0:13,0:13:30	0/0:13,0:13:30	0/0:18,0:18:40	0/0:24,0:24:60	0/0:25,0:25:60	0/0:12,0:12:30	0/0:28,0:28:60	0/0:25,0:25:40	0/0:16,0:16:40	0/0:27,0:27:60	0/0:15,0:15:10	0/0:20,0:20:50	0/0:22,0:22:60	0/0:21,0:21:50	0/0:27,0:27:60	0/0:24,0:24:60	0/0:28,0:28:60	0/0:26,0:26:60	0/0:23,0:23:50	0/0:31,0:31:60	0/0:24,0:24:60	0/0:12,0:12:30	0/0:30,0:30:60	0/0:18,0:18:40	0/0:31,0:31:60	0/0:24,0:24:60	0/0:21,0:21:60	0/0:17,0:17:40	0/0:20,0:20:40	0/0:19,0:19:50	0/0:21,0:21:50	0/0:13,0:13:30	0/0:36,0:36:60	0/0:30,0:30:60	0/1:15,10:25:99:212,0,384	0/0:29,0:29:60
+chr1	943136	rs201043644	GA	G	551.35	PASS	AC=2;AF=0.015;AN=130;AS_BaseQRankSum=.;AS_FS=0.000;AS_FilterStatus=PASS;AS_InbreedingCoeff=0.8072;AS_MQ=60.00;AS_MQRankSum=.;AS_QD=30.61;AS_ReadPosRankSum=.;AS_SOR=0.914;AS_VQSLOD=3.2508;AS_culprit=AS_FS;DB;DP=957;ExcessHet=0.0000;FS=0.000;InbreedingCoeff=0.7976;MLEAC=2;MLEAF=0.015;MQ=60.00;POSITIVE_TRAIN_SITE;QD=30.63;SOR=0.914	GT:AD:DP:GQ:PL	0/0:24,0:24:50	0/0:27,0:27:60	0/0:18,0:18:50	0/0:28,0:28:60	1/1:0,18:18:54:588,54,0	0/0:15,0:15:30	0/0:15,0:15:30	0/0:22,0:22:50	0/0:12,0:12:20	0/0:15,0:15:30	0/0:13,0:13:30	0/0:11,0:11:20	0/0:14,0:14:30	0/0:13,0:13:30	0/0:12,0:12:20	0/0:19,0:19:40	0/0:9,0:9:20	0/0:15,0:15:30	0/0:18,0:18:40	0/0:12,0:12:30	0/0:11,0:11:20	0/0:12,0:12:30	0/0:18,0:18:40	0/0:18,0:18:30	0/0:17,0:17:40	0/0:11,0:11:20	0/0:18,0:18:40	0/0:17,0:17:40	0/0:14,0:14:30	0/0:8,0:8:20	0/0:10,0:10:20	0/0:18,0:18:40	0/0:10,0:10:20	0/0:13,0:13:30	0/0:14,0:14:30	0/0:22,0:22:50	0/0:13,0:13:30	0/0:13,0:13:30	0/0:10,0:10:20	0/0:8,0:8:10	0/0:17,0:17:40	0/0:12,0:12:20	0/0:15,0:15:30	0/0:13,0:13:30	0/0:18,0:18:40	0/0:14,0:14:30	0/0:17,0:17:10	0/0:9,0:9:20	0/0:13,0:13:30	0/0:17,0:17:40	0/0:11,0:11:20	0/0:20,0:20:40	0/0:12,0:12:20	0/0:14,0:14:30	0/0:14,0:14:40	0/0:10,0:10:20	0/0:11,0:11:20	0/0:13,0:13:30	0/0:15,0:15:30	0/0:13,0:13:30	0/0:14,0:14:30	0/0:12,0:12:20	0/0:19,0:19:40	0/0:8,0:8:10	0/0:21,0:21:50
+chr1	943365	rs72902602	A	C	661.62	PASS	AC=1;AF=7.692e-03;AN=130;AS_BaseQRankSum=0.200;AS_FS=0.000;AS_FilterStatus=PASS;AS_InbreedingCoeff=-0.0078;AS_MQ=60.00;AS_MQRankSum=0.000;AS_QD=10.68;AS_ReadPosRankSum=0.400;AS_SOR=0.811;AS_VQSLOD=9.5103;AS_culprit=AS_MQ;BaseQRankSum=0.245;DB;DP=2151;ExcessHet=0.0000;FS=0.000;InbreedingCoeff=-0.0078;MLEAC=1;MLEAF=7.692e-03;MQ=60.00;MQRankSum=0.00;QD=10.67;ReadPosRankSum=0.467;SOR=0.811	GT:AD:DP:GQ:PL	0/0:30,0:30:60	0/0:16,0:16:30	0/0:25,0:25:50	0/0:22,0:22:50	0/1:28,34:62:99:680,0,527	0/0:36,0:36:60	0/0:33,0:33:60	0/0:29,0:29:60	0/0:32,0:32:60	0/0:34,0:34:60	0/0:34,0:34:60	0/0:31,0:31:60	0/0:34,0:34:60	0/0:30,0:30:60	0/0:31,0:31:60	0/0:37,0:37:60	0/0:32,0:32:60	0/0:34,0:34:60	0/0:37,0:37:60	0/0:34,0:34:60	0/0:36,0:36:60	0/0:34,0:34:60	0/0:32,0:32:60	0/0:31,0:31:60	0/0:34,0:34:60	0/0:33,0:33:60	0/0:38,0:38:60	0/0:31,0:31:60	0/0:31,0:31:60	0/0:34,0:34:60	0/0:30,0:30:60	0/0:37,0:37:60	0/0:31,0:31:60	0/0:32,0:32:60	0/0:33,0:33:60	0/0:35,0:35:60	0/0:32,0:32:60	0/0:31,0:31:60	0/0:36,0:36:60	0/0:34,0:34:60	0/0:31,0:31:60	0/0:33,0:33:60	0/0:35,0:35:60	0/0:34,0:34:60	0/0:32,0:32:60	0/0:35,0:35:60	0/0:34,0:34:60	0/0:33,0:33:60	0/0:36,0:36:60	0/0:34,0:34:60	0/0:34,0:34:60	0/0:31,0:31:60	0/0:33,0:33:60	0/0:35,0:35:60	0/0:31,0:31:60	0/0:36,0:36:60	0/0:32,0:32:60	0/0:34,0:34:60	0/0:34,0:34:60	0/0:30,0:30:60	0/0:34,0:34:60	0/0:33,0:33:60	0/0:33,0:33:60	0/0:32,0:32:60	0/0:33,0:33:60
+chr1	943429	rs191952374	C	T	1116.29	PASS	AC=2;AF=0.015;AN=130;AS_BaseQRankSum=1.700;AS_FS=7.671;AS_FilterStatus=PASS;AS_InbreedingCoeff=-0.0156;AS_MQ=60.00;AS_MQRankSum=0.000;AS_QD=15.08;AS_ReadPosRankSum=0.600;AS_SOR=2.124;AS_VQSLOD=5.2137;AS_culprit=AS_MQ;BaseQRankSum=2.01;DB;DP=2074;ExcessHet=0.0338;FS=7.671;InbreedingCoeff=-0.0156;MLEAC=2;MLEAF=0.015;MQ=60.00;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=15.08;ReadPosRankSum=1.48;SOR=2.124	GT:AD:DP:GQ:PL	0/0:18,0:18:50	0/0:16,0:16:40	0/0:16,0:16:40	0/0:15,0:15:40	0/0:22,0:22:50	0/0:36,0:36:60	0/0:33,0:33:60	0/0:29,0:29:60	0/0:32,0:32:60	0/0:34,0:34:60	0/0:34,0:34:60	0/0:31,0:31:60	0/0:34,0:34:60	0/0:30,0:30:60	0/0:31,0:31:60	0/0:37,0:37:60	0/0:32,0:32:60	0/0:34,0:34:60	0/0:37,0:37:60	0/0:34,0:34:60	0/0:36,0:36:60	0/0:34,0:34:60	0/0:32,0:32:60	0/0:31,0:31:60	0/0:34,0:34:60	0/0:33,0:33:60	0/0:34,0:34:60	0/0:31,0:31:60	0/0:31,0:31:60	0/1:18,16:34:99:454,0,483	0/0:30,0:30:60	0/0:37,0:37:60	0/0:31,0:31:60	0/0:32,0:32:60	0/0:33,0:33:60	0/0:35,0:35:60	0/0:32,0:32:60	0/0:31,0:31:60	0/0:36,0:36:60	0/0:34,0:34:60	0/0:22,0:22:40	0/0:33,0:33:60	0/0:35,0:35:60	0/0:34,0:34:60	0/0:32,0:32:60	0/1:16,24:40:99:693,0,395	0/0:34,0:34:60	0/0:33,0:33:60	0/0:36,0:36:60	0/0:34,0:34:60	0/0:34,0:34:60	0/0:31,0:31:60	0/0:33,0:33:60	0/0:35,0:35:60	0/0:31,0:31:60	0/0:36,0:36:60	0/0:32,0:32:60	0/0:34,0:34:60	0/0:34,0:34:60	0/0:30,0:30:60	0/0:34,0:34:60	0/0:33,0:33:60	0/0:33,0:33:60	0/0:32,0:32:60	0/0:33,0:33:60
+chr1	943937	rs7523549	C	T	984.62	PASS	AC=1;AF=7.692e-03;AN=130;AS_BaseQRankSum=0.800;AS_FS=6.350;AS_FilterStatus=PASS;AS_InbreedingCoeff=-0.0078;AS_MQ=60.00;AS_MQRankSum=0.000;AS_QD=14.28;AS_ReadPosRankSum=-1.800;AS_SOR=1.118;AS_VQSLOD=5.2667;AS_culprit=AS_MQ;BaseQRankSum=0.837;DB;DP=2269;ExcessHet=0.0000;FS=6.350;InbreedingCoeff=-0.0078;MLEAC=1;MLEAF=7.692e-03;MQ=60.00;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=14.27;ReadPosRankSum=-1.755e+00;SOR=1.118	GT:AD:DP:GQ:PL	0/0:30,0:30:60	0/0:37,0:37:60	0/0:31,0:31:60	0/0:31,0:31:60	0/0:29,0:29:60	0/0:32,0:32:60	0/0:35,0:35:60	0/0:43,0:43:60	0/0:31,0:31:60	0/0:36,0:36:60	0/0:34,0:34:60	0/0:32,0:32:60	0/0:36,0:36:60	0/0:37,0:37:60	0/0:39,0:39:60	0/0:40,0:40:60	0/0:32,0:32:60	0/0:33,0:33:60	0/0:33,0:33:60	0/0:34,0:34:60	0/0:33,0:33:60	0/0:37,0:37:60	0/0:41,0:41:60	0/0:35,0:35:60	0/0:36,0:36:60	0/0:33,0:33:60	0/0:33,0:33:60	0/0:34,0:34:60	0/0:31,0:31:60	0/0:36,0:36:60	0/0:34,0:34:60	0/0:34,0:34:60	0/0:31,0:31:60	0/0:34,0:34:60	0/0:40,0:40:60	0/0:35,0:35:60	0/0:36,0:36:60	0/0:37,0:37:60	0/0:33,0:33:60	0/0:32,0:32:60	0/0:32,0:32:60	0/0:38,0:38:60	0/0:37,0:37:60	0/0:31,0:31:60	0/0:38,0:38:60	0/0:41,0:41:60	0/0:37,0:37:60	0/0:35,0:35:60	0/0:36,0:36:60	0/1:33,36:69:99:1003,0,879	0/0:34,0:34:60	0/0:33,0:33:60	0/0:33,0:33:60	0/0:32,0:32:60	0/0:31,0:31:60	0/0:33,0:33:60	0/0:32,0:32:60	0/0:31,0:31:60	0/0:31,0:31:60	0/0:32,0:32:60	0/0:30,0:30:60	0/0:32,0:32:60	0/0:37,0:37:60	0/0:36,0:36:60	0/0:38,0:38:60
+chr1	944795	.	C	T	296.62	PASS	AC=1;AF=7.692e-03;AN=130;AS_BaseQRankSum=-1.800;AS_FS=0.000;AS_FilterStatus=PASS;AS_InbreedingCoeff=-0.0078;AS_MQ=60.00;AS_MQRankSum=1.500;AS_QD=12.38;AS_ReadPosRankSum=0.300;AS_SOR=0.317;AS_VQSLOD=-0.3892;AS_culprit=AS_MQRankSum;BaseQRankSum=-1.762e+00;DP=1918;ExcessHet=0.0000;FS=0.000;InbreedingCoeff=-0.0078;MLEAC=1;MLEAF=7.692e-03;MQ=58.66;MQRankSum=1.51;QD=12.36;ReadPosRankSum=0.318;SOR=0.317	GT:AD:DP:GQ:PL	0/0:31,0:31:60	0/0:34,0:34:60	0/0:34,0:34:60	0/0:28,0:28:60	0/0:13,0:13:30	0/0:32,0:32:60	0/0:32,0:32:60	0/0:36,0:36:60	0/0:29,0:29:60	0/0:34,0:34:60	0/0:31,0:31:60	0/0:32,0:32:60	0/0:31,0:31:60	0/0:35,0:35:60	0/0:35,0:35:60	0/0:33,0:33:60	0/0:28,0:28:60	0/0:32,0:32:60	0/1:12,12:24:99:315,0,342	0/0:26,0:26:50	0/0:24,0:24:50	0/0:16,0:16:30	0/0:34,0:34:60	0/0:30,0:30:60	0/0:34,0:34:60	0/0:27,0:27:60	0/0:28,0:28:60	0/0:28,0:28:60	0/0:30,0:30:60	0/0:19,0:19:30	0/0:33,0:33:60	0/0:31,0:31:60	0/0:26,0:26:60	0/0:20,0:20:40	0/0:38,0:38:60	0/0:36,0:36:60	0/0:30,0:30:60	0/0:28,0:28:60	0/0:23,0:23:50	0/0:34,0:34:60	0/0:35,0:35:60	0/0:31,0:31:60	0/0:38,0:38:60	0/0:35,0:35:60	0/0:27,0:27:60	0/0:31,0:31:60	0/0:26,0:26:60	0/0:23,0:23:50	0/0:24,0:24:50	0/0:25,0:25:60	0/0:36,0:36:60	0/0:35,0:35:60	0/0:34,0:34:60	0/0:35,0:35:60	0/0:26,0:26:60	0/0:32,0:32:60	0/0:34,0:34:60	0/0:27,0:27:60	0/0:28,0:28:60	0/0:34,0:34:60	0/0:27,0:27:60	0/0:19,0:19:40	0/0:20,0:20:50	0/0:26,0:26:60	0/0:30,0:30:60
+chr1	945010	rs3748593	C	A	531.62	PASS	AC=1;AF=7.692e-03;AN=130;AS_BaseQRankSum=1.800;AS_FS=0.000;AS_FilterStatus=PASS;AS_InbreedingCoeff=-0.0078;AS_MQ=60.00;AS_MQRankSum=0.000;AS_QD=10.64;AS_ReadPosRankSum=-0.700;AS_SOR=0.632;AS_VQSLOD=10.3507;AS_culprit=AS_MQ;BaseQRankSum=1.83;DB;DP=2238;ExcessHet=0.0000;FS=0.000;InbreedingCoeff=-0.0078;MLEAC=1;MLEAF=7.692e-03;MQ=60.00;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=10.63;ReadPosRankSum=-6.690e-01;SOR=0.632	GT:AD:DP:GQ:PL	0/0:36,0:36:60	0/0:30,0:30:60	0/0:34,0:34:60	0/0:37,0:37:60	0/0:27,0:27:60	0/0:36,0:36:60	0/0:38,0:38:60	0/0:35,0:35:60	0/0:35,0:35:60	0/0:30,0:30:60	0/0:34,0:34:60	0/0:32,0:32:60	0/0:30,0:30:60	0/0:39,0:39:60	0/0:32,0:32:60	0/0:31,0:31:60	0/0:32,0:32:60	0/0:29,0:29:60	0/0:37,0:37:60	0/0:31,0:31:60	0/0:33,0:33:60	0/0:33,0:33:60	0/0:35,0:35:60	0/0:32,0:32:60	0/0:33,0:33:60	0/0:36,0:36:60	0/0:35,0:35:60	0/0:34,0:34:60	0/0:34,0:34:60	0/0:33,0:33:60	0/0:37,0:37:60	0/0:32,0:32:60	0/0:34,0:34:60	0/0:29,0:29:60	0/0:34,0:34:60	0/0:33,0:33:60	0/0:31,0:31:60	0/0:40,0:40:60	0/0:36,0:36:60	0/0:35,0:35:60	0/0:33,0:33:60	0/0:33,0:33:60	0/0:31,0:31:60	0/0:34,0:34:60	0/0:34,0:34:60	0/0:34,0:34:60	0/0:66,0:66:60	0/0:37,0:37:60	0/0:31,0:31:60	0/1:29,21:50:99:550,0,746	0/0:32,0:32:60	0/0:35,0:35:60	0/0:32,0:32:60	0/0:35,0:35:60	0/0:33,0:33:60	0/0:36,0:36:60	0/0:40,0:40:60	0/0:34,0:34:60	0/0:31,0:31:60	0/0:41,0:41:60	0/0:35,0:35:60	0/0:33,0:33:60	0/0:36,0:36:60	0/0:31,0:31:60	0/0:27,0:27:60
+chr1	945086	rs138652036	T	C	479.62	PASS	AC=1;AF=7.692e-03;AN=130;AS_BaseQRankSum=-0.400;AS_FS=5.931;AS_FilterStatus=PASS;AS_InbreedingCoeff=-0.0078;AS_MQ=60.00;AS_MQRankSum=0.000;AS_QD=9.60;AS_ReadPosRankSum=-2.100;AS_SOR=0.162;AS_VQSLOD=3.5600;AS_culprit=AS_ReadPosRankSum;BaseQRankSum=-3.330e-01;DB;DP=2188;ExcessHet=0.0000;FS=5.931;InbreedingCoeff=-0.0078;MLEAC=1;MLEAF=7.692e-03;MQ=60.00;MQRankSum=0.00;QD=9.59;ReadPosRankSum=-2.087e+00;SOR=0.162	GT:AD:DP:GQ:PL	0/0:36,0:36:60	0/0:30,0:30:60	0/0:34,0:34:60	0/0:37,0:37:60	0/0:27,0:27:60	0/0:36,0:36:60	0/0:38,0:38:60	0/0:35,0:35:60	0/0:35,0:35:60	0/0:30,0:30:60	0/0:34,0:34:60	0/0:32,0:32:60	0/0:30,0:30:60	0/0:39,0:39:60	0/0:32,0:32:60	0/0:31,0:31:60	0/0:32,0:32:60	0/0:29,0:29:60	0/0:24,0:24:50	0/0:31,0:31:60	0/0:33,0:33:60	0/0:33,0:33:60	0/0:35,0:35:60	0/0:32,0:32:60	0/0:33,0:33:60	0/0:36,0:36:60	0/0:35,0:35:60	0/0:34,0:34:60	0/0:34,0:34:60	0/0:33,0:33:60	0/0:37,0:37:60	0/0:32,0:32:60	0/0:34,0:34:60	0/0:29,0:29:60	0/0:34,0:34:60	0/0:33,0:33:60	0/0:31,0:31:60	0/0:40,0:40:60	0/0:36,0:36:60	0/0:35,0:35:60	0/0:33,0:33:60	0/0:33,0:33:60	0/0:31,0:31:60	0/0:34,0:34:60	0/0:34,0:34:60	0/0:34,0:34:60	0/1:29,21:50:99:498,0,759	0/0:37,0:37:60	0/0:31,0:31:60	0/0:39,0:39:60	0/0:32,0:32:60	0/0:35,0:35:60	0/0:32,0:32:60	0/0:35,0:35:60	0/0:33,0:33:60	0/0:36,0:36:60	0/0:30,0:30:60	0/0:34,0:34:60	0/0:31,0:31:60	0/0:41,0:41:60	0/0:35,0:35:60	0/0:33,0:33:60	0/0:36,0:36:60	0/0:31,0:31:60	0/0:27,0:27:60
+chr1	945573	rs138129954	G	A	2776.29	PASS	AC=2;AF=0.015;AN=130;AS_BaseQRankSum=0.150;AS_FS=0.000;AS_FilterStatus=PASS;AS_InbreedingCoeff=-0.0156;AS_MQ=54.63;AS_MQRankSum=-0.550;AS_QD=11.24;AS_ReadPosRankSum=-0.300;AS_SOR=0.730;AS_VQSLOD=2.3446;AS_culprit=AS_MQ;BaseQRankSum=1.39;DB;DP=2431;ExcessHet=0.0338;FS=0.000;InbreedingCoeff=-0.0156;MLEAC=2;MLEAF=0.015;MQ=54.82;MQRankSum=0.333;QD=11.24;ReadPosRankSum=0.030;SOR=0.730	GT:AD:DP:GQ:PL	0/0:36,0:36:60	0/0:33,0:33:60	0/0:39,0:39:60	0/0:30,0:30:60	0/0:29,0:29:60	0/0:33,0:33:60	0/0:30,0:30:60	0/0:35,0:35:60	0/0:37,0:37:60	0/0:28,0:28:60	0/0:32,0:32:60	0/1:66,52:118:99:1263,0,1714	0/0:30,0:30:60	0/0:36,0:36:60	0/0:64,0:64:60	0/0:34,0:34:60	0/0:36,0:36:60	0/0:32,0:32:60	0/0:35,0:35:60	0/0:32,0:32:60	0/0:32,0:32:60	0/0:28,0:28:60	0/0:30,0:30:60	0/0:32,0:32:60	0/0:34,0:34:60	0/0:32,0:32:60	0/0:28,0:28:60	0/0:34,0:34:60	0/0:31,0:31:60	0/0:31,0:31:60	0/0:32,0:32:60	0/0:31,0:31:60	0/0:31,0:31:60	0/0:34,0:34:60	0/0:32,0:32:60	0/0:38,0:38:60	0/0:117,0:117:60	0/0:26,0:26:60	0/0:33,0:33:60	0/0:32,0:32:60	0/1:71,58:129:99:1544,0,1802	0/0:34,0:34:60	0/0:37,0:37:60	0/0:33,0:33:60	0/0:34,0:34:60	0/0:33,0:33:60	0/0:66,0:66:60	0/0:34,0:34:60	0/0:31,0:31:60	0/0:33,0:33:60	0/0:28,0:28:60	0/0:29,0:29:60	0/0:34,0:34:60	0/0:30,0:30:60	0/0:34,0:34:60	0/0:32,0:32:60	0/0:34,0:34:60	0/0:35,0:35:60	0/0:31,0:31:60	0/0:27,0:27:60	0/0:33,0:33:60	0/0:30,0:30:60	0/0:34,0:34:60	0/0:28,0:28:60	0/0:31,0:31:60
+chr1	945670	rs374558436	C	T	1359.62	PASS	AC=1;AF=7.692e-03;AN=130;AS_BaseQRankSum=-3.400;AS_FS=0.911;AS_FilterStatus=PASS;AS_InbreedingCoeff=-0.0078;AS_MQ=60.00;AS_MQRankSum=0.000;AS_QD=14.47;AS_ReadPosRankSum=0.300;AS_SOR=0.581;AS_VQSLOD=7.2592;AS_culprit=AS_MQ;BaseQRankSum=-3.393e+00;DB;DP=2288;ExcessHet=0.0000;FS=0.911;InbreedingCoeff=-0.0078;MLEAC=1;MLEAF=7.692e-03;MQ=60.00;MQRankSum=0.00;QD=14.46;ReadPosRankSum=0.320;SOR=0.581	GT:AD:DP:GQ:PL	0/0:36,0:36:60	0/0:33,0:33:60	0/0:39,0:39:60	0/0:30,0:30:60	0/0:29,0:29:60	0/0:33,0:33:60	0/0:30,0:30:60	0/0:35,0:35:60	0/0:37,0:37:60	0/0:28,0:28:60	0/0:32,0:32:60	0/0:38,0:38:60	0/0:30,0:30:60	0/0:36,0:36:60	0/0:64,0:64:60	0/0:34,0:34:60	0/0:36,0:36:60	0/0:32,0:32:60	0/0:35,0:35:60	0/0:32,0:32:60	0/0:32,0:32:60	0/0:28,0:28:60	0/0:30,0:30:60	0/0:32,0:32:60	0/0:34,0:34:60	0/0:32,0:32:60	0/0:28,0:28:60	0/0:34,0:34:60	0/0:31,0:31:60	0/0:31,0:31:60	0/0:32,0:32:60	0/0:31,0:31:60	0/0:31,0:31:60	0/0:34,0:34:60	0/0:32,0:32:60	0/0:38,0:38:60	0/0:117,0:117:60	0/0:26,0:26:60	0/0:33,0:33:60	0/0:32,0:32:60	0/0:38,0:38:60	0/0:34,0:34:60	0/0:37,0:37:60	0/0:33,0:33:60	0/0:34,0:34:60	0/0:33,0:33:60	0/1:41,53:94:99:1378,0,1117	0/0:34,0:34:60	0/0:31,0:31:60	0/0:33,0:33:60	0/0:28,0:28:60	0/0:29,0:29:60	0/0:34,0:34:60	0/0:30,0:30:60	0/0:34,0:34:60	0/0:32,0:32:60	0/0:34,0:34:60	0/0:35,0:35:60	0/0:31,0:31:60	0/0:27,0:27:60	0/0:33,0:33:60	0/0:30,0:30:60	0/0:34,0:34:60	0/0:28,0:28:60	0/0:31,0:31:60
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/actual.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/actual.vcf.idx
new file mode 100644
index 00000000000..25654979306
Binary files /dev/null and b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/actual.vcf.idx differ
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/diploid.rb.g.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/diploid.rb.g.vcf
new file mode 100644
index 00000000000..feb190f76b7
--- /dev/null
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/diploid.rb.g.vcf
@@ -0,0 +1,64 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths (counting only informative reads out of the total reads) for the ref and alt alleles in the order listed">
+##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele fractions for alt alleles in the order listed">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
+##FORMAT=<ID=F1R2,Number=R,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting each allele">
+##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele">
+##FORMAT=<ID=GP,Number=G,Type=Float,Description="Phred-scaled posterior probabilities for genotypes as defined in the VCF specification">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=ICNT,Number=2,Type=Integer,Description="Counts of INDEL informative reads based on the reference confidence model">
+##FORMAT=<ID=MB,Number=4,Type=Integer,Description="Per-sample component statistics to detect mate bias">
+##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##FORMAT=<ID=PRI,Number=G,Type=Float,Description="Phred-scaled prior probabilities for genotypes">
+##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
+##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias">
+##FORMAT=<ID=SPL,Number=.,Type=Integer,Description="Normalized, Phred-scaled likelihoods for SNPs based on the reference confidence model">
+##FORMAT=<ID=SQ,Number=1,Type=Float,Description="Somatic quality">
+##GVCFBlock0-20=minGQ=0(inclusive),maxGQ=20(exclusive)
+##GVCFBlock20-30=minGQ=20(inclusive),maxGQ=30(exclusive)
+##GVCFBlock30-40=minGQ=30(inclusive),maxGQ=40(exclusive)
+##GVCFBlock40-100=minGQ=40(inclusive),maxGQ=100(exclusive)
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=AS_BaseQRankSum,Number=A,Type=Float,Description="allele specific Z-score from Wilcoxon rank sum test of each Alt Vs. Ref base qualities">
+##INFO=<ID=AS_FS,Number=A,Type=Float,Description="allele specific phred-scaled p-value using Fisher's exact test to detect strand bias of each alt allele">
+##INFO=<ID=AS_InbreedingCoeff,Number=A,Type=Float,Description="Allele-specific inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
+##INFO=<ID=AS_MQ,Number=A,Type=Float,Description="Allele-specific RMS Mapping Quality">
+##INFO=<ID=AS_MQRankSum,Number=A,Type=Float,Description="Allele-specific Mapping Quality Rank Sum">
+##INFO=<ID=AS_QD,Number=A,Type=Float,Description="Allele-specific Variant Confidence/Quality by Depth">
+##INFO=<ID=AS_QUALapprox,Number=1,Type=String,Description="Allele-specific QUAL approximations">
+##INFO=<ID=AS_ReadPosRankSum,Number=A,Type=Float,Description="allele specific Z-score from Wilcoxon rank sum test of each Alt vs. Ref read position bias">
+##INFO=<ID=AS_SOR,Number=A,Type=Float,Description="Allele specific strand Odds Ratio of 2x|Alts| contingency table to detect allele specific strand bias">
+##INFO=<ID=AS_VarDP,Number=1,Type=String,Description="Allele-specific (informative) depth over variant genotypes -- including ref, RAW format">
+##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (informative and non-informative); some reads may have been filtered based on mapq etc.">
+##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
+##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
+##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
+##INFO=<ID=FractionInformativeReads,Number=1,Type=Float,Description="The fraction of informative reads out of the total reads">
+##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
+##INFO=<ID=LOD,Number=1,Type=Float,Description="Variant LOD score">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
+##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
+##INFO=<ID=MQ_DP,Number=1,Type=Integer,Description="Depth over variant samples for better MQ calculation (deprecated -- use RAW_MQandDP instead.)">
+##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
+##INFO=<ID=QUALapprox,Number=1,Type=Integer,Description="Sum of PL[0] values; used to approximate the QUAL score">
+##INFO=<ID=R2_5P_bias,Number=1,Type=Float,Description="Score based on mate bias and distance from 5 prime end">
+##INFO=<ID=RAW_GT_COUNT,Number=3,Type=Integer,Description="Counts of genotypes w.r.t. the reference allele in the following order: 0/0, 0/*, */*, i.e. all alts lumped together; for use in calculating excess heterozygosity">
+##INFO=<ID=RAW_MQandDP,Number=2,Type=Integer,Description="Raw data (sum of squared MQ and total depth) for improved RMS Mapping Quality calculation. Incompatible with deprecated RAW_MQ formulation.">
+##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
+##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
+##INFO=<ID=VarDP,Number=1,Type=Integer,Description="(informative) depth over variant genotypes">
+##contig=<ID=chrX,length=156040895>
+##reference=file:///seq/dragen/references/GRCh38dh/v3.7.8/reference.bin
+##source=ReblockGVCF
+##bcftools_viewVersion=1.19+htslib-1.19
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	haploid
+chrX	66780645	.	C	CT,<NON_REF>	65.55	.	AS_QUALapprox=|71|0;AS_VarDP=0|4|0;DP=9;MQ=216.86;QUALapprox=71;RAW_GT_COUNT=0,0,1;RAW_MQandDP=423254,9;VarDP=4	GT:AD:AF:DP:F1R2:F2R1:GQ:ICNT:MB:PL:SB	1/1:0,4,0:1,0:4:0,1,0:0,3,0:71:0,4:0,0,2,2,1,1:71,0,89
+chrX	66780646	.	T	TA,<NON_REF>	44.8	.	AS_QUALapprox=|50|0;AS_VarDP=13|8|0;DP=30;MQ=218.46;QUALapprox=50;RAW_GT_COUNT=0,1,0;RAW_MQandDP=1431743,30;VarDP=21	GT:AD:AF:DP:F1R2:F2R1:GQ:ICNT:MB:PL:SB	1:0,4,0:1,0:4:0,1,0:0,3,0:71:0,4:0,0,2,2:71,0,89
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/diploid.rb.g.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/diploid.rb.g.vcf.idx
new file mode 100644
index 00000000000..2acdf9a2707
Binary files /dev/null and b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/diploid.rb.g.vcf.idx differ
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/expected.NA12878.rb.g.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/expected.NA12878.rb.g.vcf
new file mode 100644
index 00000000000..790563325a7
--- /dev/null
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/expected.NA12878.rb.g.vcf
@@ -0,0 +1,3508 @@
+##fileformat=VCFv4.2
+##ALT=<ID=NON_REF,Description="Represents any possible alternative allele not already represented at this location by REF and ALT">
+##FILTER=<ID=LowQual,Description="Low quality">
+##FILTER=<ID=PASS,Description="All filters passed">
+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
+##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another; will always be heterozygous and is not intended to describe called alleles">
+##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)">
+##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
+##GATKCommandLine=<ID=HaplotypeCaller,CommandLine="HaplotypeCaller --gvcf-gq-bands 10 --gvcf-gq-bands 20 --gvcf-gq-bands 30 --gvcf-gq-bands 40 --gvcf-gq-bands 50 --gvcf-gq-bands 60 --gvcf-gq-bands 70 --gvcf-gq-bands 80 --gvcf-gq-bands 90 --flow-mode ADVANCED --bam-writer-type CALLED_HAPLOTYPES_NO_READS --smith-waterman FASTEST_AVAILABLE --emit-ref-confidence GVCF --output downsampled_NA12878.g.vcf.gz --intervals /cromwell_root/broad-gotc-dev-cromwell-execution/TestUltimaGenomicsWholeGenomeGermline/e8c683c4-5bfd-4285-abcd-2cdd7899fe64/call-UltimaGenomicsWholeGenomeGermline/UltimaGenomicsWholeGenomeGermline/05337c3d-35d8-4cb0-a8eb-1c5f1023fdc0/call-ScatterIntervalList/cacheCopy/glob-cb4648beeaff920acb03de7603c06f98/199scattered.interval_list --input gs://broad-gotc-dev-cromwell-execution/TestUltimaGenomicsWholeGenomeGermline/e8c683c4-5bfd-4285-abcd-2cdd7899fe64/call-UltimaGenomicsWholeGenomeGermline/UltimaGenomicsWholeGenomeGermline/05337c3d-35d8-4cb0-a8eb-1c5f1023fdc0/call-UltimaGenomicsWholeGenomeCramOnly/UltimaGenomicsWholeGenomeCramOnly/1056a0d1-9910-4911-9118-3018a8255127/call-AlignmentAndMarkDuplicates/AlignmentAndMarkDuplicates/fc2194ac-ae9d-4c25-878e-a6b9dfc80c20/call-MarkDuplicatesSpark/downsampled_NA12878.aligned.sorted.duplicates_marked.bam --read-index /cromwell_root/broad-gotc-dev-cromwell-execution/TestUltimaGenomicsWholeGenomeGermline/e8c683c4-5bfd-4285-abcd-2cdd7899fe64/call-UltimaGenomicsWholeGenomeGermline/UltimaGenomicsWholeGenomeGermline/05337c3d-35d8-4cb0-a8eb-1c5f1023fdc0/call-UltimaGenomicsWholeGenomeCramOnly/UltimaGenomicsWholeGenomeCramOnly/1056a0d1-9910-4911-9118-3018a8255127/call-AlignmentAndMarkDuplicates/AlignmentAndMarkDuplicates/fc2194ac-ae9d-4c25-878e-a6b9dfc80c20/call-MarkDuplicatesSpark/downsampled_NA12878.aligned.sorted.duplicates_marked.bam.bai --reference /cromwell_root/gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta --annotation AssemblyComplexity --annotation-group StandardAnnotation --annotation-group StandardHCAnnotation --annotation-group AS_StandardAnnotation --assembly-complexity-reference-mode true --use-posteriors-to-calculate-qual false --dont-use-dragstr-priors false --use-new-qual-calculator true --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --genotype-assignment-method USE_PLS_TO_ASSIGN --contamination-fraction-to-filter 0.0 --output-mode EMIT_VARIANTS_ONLY --all-site-pls false --flow-likelihood-parallel-threads 0 --flow-likelihood-optimized-comp false --trim-to-haplotype true --exact-matching false --flow-use-t0-tag false --flow-probability-threshold 0.003 --flow-remove-non-single-base-pair-indels false --flow-remove-one-zero-probs false --flow-quantization-bins 121 --flow-fill-empty-bins-value 0.001 --flow-symmetric-indel-probs false --flow-report-insertion-or-deletion false --flow-disallow-probs-larger-than-call false --flow-lump-probs false --flow-retain-max-n-probs-base-format false --flow-probability-scaling-factor 10 --flow-order-cycle-length 4 --keep-boundary-flows false --floor-blocks false --indel-size-to-eliminate-in-ref-model 10 --disable-optimizations false --dragen-mode false --dragen-378-concordance-mode false --apply-bqd false --apply-frd false --disable-spanning-event-genotyping false --transform-dragen-mapping-quality false --mapping-quality-threshold-for-genotyping 20 --max-effective-depth-adjustment-for-frd 0 --just-determine-active-regions false --dont-genotype false --do-not-run-physical-phasing false --do-not-correct-overlapping-quality false --use-filtered-reads-for-annotations false --use-flow-aligner-for-stepwise-hc-filtering false --adaptive-pruning false --do-not-recover-dangling-branches false --recover-dangling-heads false --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --pruning-seeding-lod-threshold 9.210340371976184 --max-unpruned-variants 100 --linked-de-bruijn-graph false --disable-artificial-haplotype-recovery false --enable-legacy-graph-cycle-detection false --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --num-matching-bases-in-dangling-end-to-recover -1 --error-correction-log-odds -Infinity --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --dragstr-het-hom-ratio 2 --dont-use-dragstr-pair-hmm-scores false --pair-hmm-gap-continuation-penalty 10 --expected-mismatch-rate-for-read-disqualification 0.02 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --disable-symmetric-hmm-normalizing false --disable-cap-base-qualities-to-map-quality false --enable-dynamic-read-disqualification-for-genotyping false --dynamic-read-disqualification-threshold 1.0 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --flow-hmm-engine-min-indel-adjust 6 --flow-hmm-engine-flat-insertion-penatly 45 --flow-hmm-engine-flat-deletion-penatly 45 --pileup-detection false --use-pdhmm false --use-pdhmm-overlap-optimization false --make-determined-haps-from-pd-code false --print-pileupcalling-status false --fallback-gga-if-pdhmm-fails true --pileup-detection-enable-indel-pileup-calling false --pileup-detection-active-region-phred-threshold 0.0 --num-artificial-haplotypes-to-add-per-allele 5 --artifical-haplotype-filtering-kmer-size 10 --pileup-detection-snp-alt-threshold 0.1 --pileup-detection-indel-alt-threshold 0.1 --pileup-detection-absolute-alt-depth 0.0 --pileup-detection-snp-adjacent-to-assembled-indel-range 5 --pileup-detection-snp-basequality-filter 12 --pileup-detection-bad-read-tolerance 0.0 --pileup-detection-proper-pair-read-badness true --pileup-detection-edit-distance-read-badness-threshold 0.08 --pileup-detection-chimeric-read-badness true --pileup-detection-template-mean-badness-threshold 0.0 --pileup-detection-template-std-badness-threshold 0.0 --pileup-detection-filter-assembly-alt-bad-read-tolerance 0.0 --pileup-detection-edit-distance-read-badness-for-assembly-filtering-threshold 0.12 --dont-use-soft-clipped-bases false --override-fragment-softclip-check false --min-base-quality-score 10 --max-mnp-distance 0 --force-call-filtered-alleles false --reference-model-deletion-quality 30 --soft-clip-low-quality-ends false --allele-informative-reads-overlap-margin 2 --smith-waterman-dangling-end-match-value 25 --smith-waterman-dangling-end-mismatch-penalty -50 --smith-waterman-dangling-end-gap-open-penalty -110 --smith-waterman-dangling-end-gap-extend-penalty -6 --smith-waterman-haplotype-to-reference-match-value 200 --smith-waterman-haplotype-to-reference-mismatch-penalty -150 --smith-waterman-haplotype-to-reference-gap-open-penalty -260 --smith-waterman-haplotype-to-reference-gap-extend-penalty -11 --smith-waterman-read-to-haplotype-match-value 10 --smith-waterman-read-to-haplotype-mismatch-penalty -15 --smith-waterman-read-to-haplotype-gap-open-penalty -30 --smith-waterman-read-to-haplotype-gap-extend-penalty -5 --flow-assembly-collapse-hmer-size 0 --flow-assembly-collapse-partial-mode false --flow-filter-alleles false --flow-filter-alleles-qual-threshold 30.0 --flow-filter-alleles-sor-threshold 3.0 --flow-filter-lone-alleles false --flow-filter-alleles-debug-graphs false --min-assembly-region-size 50 --max-assembly-region-size 300 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --assembly-region-padding 100 --padding-around-indels 75 --padding-around-snps 20 --padding-around-strs 75 --max-extension-into-assembly-region-padding-legacy 25 --max-reads-per-alignment-start 50 --enable-legacy-assembly-region-trimming false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false --allow-old-rms-mapping-quality-annotation-data false",Version="4.5.0.0",Date="December 14, 2023 at 5:28:19 PM GMT">
+##GATKCommandLine=<ID=SelectVariants,CommandLine="SelectVariants --output expected.NA12878.rb.g.vcf --variant gs://broad-gotc-test-storage/UltimaGenomicsWholeGenomeGermline/truth/plumbing/master/NA12878.downsampled/downsampled_NA12878.annotated.rb.g.vcf.gz --intervals chr1:186475-945670 --apply-jexl-filters-first false --invertSelect false --exclude-non-variants false --exclude-filtered false --preserve-alleles false --remove-unused-alternates false --restrict-alleles-to ALL --keep-original-ac false --keep-original-dp false --mendelian-violation false --invert-mendelian-violation false --mendelian-violation-qual-threshold 0.0 --select-random-fraction 1.0 --remove-fraction-genotypes 0.0 --ignore-non-ref-in-types false --fully-decode false --max-indel-size 2147483647 --min-indel-size 0 --max-filtered-genotypes 2147483647 --min-filtered-genotypes 0 --max-fraction-filtered-genotypes 1.0 --min-fraction-filtered-genotypes 0.0 --max-nocall-number 2147483647 --max-nocall-fraction 1.0 --set-filtered-gt-to-nocall false --allow-nonoverlapping-command-line-samples false --suppress-reference-path false --fail-on-unsorted-genotype false --genomicsdb-max-alternate-alleles 50 --call-genotypes false --genomicsdb-use-bcf-codec false --genomicsdb-shared-posixfs-optimizations false --genomicsdb-use-gcs-hdfs-connector false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false",Version="4.6.0.0-19-g6a6872f-SNAPSHOT",Date="August 2, 2024 at 9:11:51 AM EDT">
+##GVCFBlock0-20=minGQ=0(inclusive),maxGQ=20(exclusive)
+##GVCFBlock20-30=minGQ=20(inclusive),maxGQ=30(exclusive)
+##GVCFBlock30-40=minGQ=30(inclusive),maxGQ=40(exclusive)
+##GVCFBlock40-100=minGQ=40(inclusive),maxGQ=100(exclusive)
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=ASSEMBLED_HAPS,Number=1,Type=Integer,Description="Haplotypes detected by the assembly region before haplotype filtering is applied">
+##INFO=<ID=AS_BaseQRankSum,Number=A,Type=Float,Description="allele specific Z-score from Wilcoxon rank sum test of each Alt Vs. Ref base qualities">
+##INFO=<ID=AS_FS,Number=A,Type=Float,Description="allele specific phred-scaled p-value using Fisher's exact test to detect strand bias of each alt allele">
+##INFO=<ID=AS_InbreedingCoeff,Number=A,Type=Float,Description="Allele-specific inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
+##INFO=<ID=AS_MQ,Number=A,Type=Float,Description="Allele-specific RMS Mapping Quality">
+##INFO=<ID=AS_MQRankSum,Number=A,Type=Float,Description="Allele-specific Mapping Quality Rank Sum">
+##INFO=<ID=AS_QD,Number=A,Type=Float,Description="Allele-specific Variant Confidence/Quality by Depth">
+##INFO=<ID=AS_QUALapprox,Number=1,Type=String,Description="Allele-specific QUAL approximations">
+##INFO=<ID=AS_RAW_BaseQRankSum,Number=1,Type=String,Description="raw data for allele specific rank sum test of base qualities">
+##INFO=<ID=AS_RAW_MQ,Number=1,Type=String,Description="Allele-specfic raw data for RMS Mapping Quality">
+##INFO=<ID=AS_RAW_MQRankSum,Number=1,Type=String,Description="Allele-specfic raw data for Mapping Quality Rank Sum">
+##INFO=<ID=AS_RAW_ReadPosRankSum,Number=1,Type=String,Description="allele specific raw data for rank sum test of read position bias">
+##INFO=<ID=AS_ReadPosRankSum,Number=A,Type=Float,Description="allele specific Z-score from Wilcoxon rank sum test of each Alt vs. Ref read position bias">
+##INFO=<ID=AS_SB_TABLE,Number=1,Type=String,Description="Allele-specific forward/reverse read counts for strand bias tests. Includes the reference and alleles separated by |.">
+##INFO=<ID=AS_SOR,Number=A,Type=Float,Description="Allele specific strand Odds Ratio of 2x|Alts| contingency table to detect allele specific strand bias">
+##INFO=<ID=AS_VarDP,Number=1,Type=String,Description="Allele-specific (informative) depth over variant genotypes -- including ref, RAW format">
+##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
+##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
+##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
+##INFO=<ID=FILTERED_HAPS,Number=1,Type=Integer,Description="Haplotypes filtered out by the haplotype filtering code">
+##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
+##INFO=<ID=HAPCOMP,Number=A,Type=Integer,Description="Edit distances of each alt allele's most common supporting haplotype from closest germline haplotype, excluding differences at the site in question.">
+##INFO=<ID=HAPDOM,Number=A,Type=Float,Description="For each alt allele, fraction of read support that best fits the most-supported haplotype containing the allele">
+##INFO=<ID=HEC,Number=.,Type=Integer,Description="Counts of support for haplotype groups excluding difference at the site in question.">
+##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
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+chr1	792417	.	C	CA,<NON_REF>	30.44	.	ASSEMBLED_HAPS=4;AS_QUALapprox=|40|0;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|4.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|0,0|0,0;AS_VarDP=0|0|0;DP=1;FILTERED_HAPS=0;QUALapprox=40;RAW_GT_COUNT=0,0,1;RAW_MQandDP=4,1;TREE_SCORE=0.372848;VarDP=1	GT:AD:DP:GQ:PGT:PID:PL:PS:SB	1|1:0,1,0:1:3:0|1:792417_C_CA:40,3,0,45,3,40:792417:0,0,1,0
+chr1	792418	.	T	<NON_REF>	.	.	END=792434	GT:DP:GQ	0/0:1:0
+chr1	792435	.	T	C,<NON_REF>	30.48	.	ASSEMBLED_HAPS=4;AS_QUALapprox=|40|0;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|4.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|0,0|0,0;AS_VarDP=0|0|0;DP=1;FILTERED_HAPS=0;QUALapprox=40;RAW_GT_COUNT=0,0,1;RAW_MQandDP=4,1;TREE_SCORE=0.913193;VarDP=1	GT:AD:DP:GQ:PGT:PID:PL:PS:SB	1|1:0,1,0:1:3:0|1:792417_C_CA:40,3,0,45,3,40:792417:0,0,1,0
+chr1	792436	.	C	<NON_REF>	.	.	END=792472	GT:DP:GQ	0/0:1:0
+chr1	792473	.	C	T,<NON_REF>	30.48	.	ASSEMBLED_HAPS=4;AS_QUALapprox=|40|0;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|4.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|0,0|0,0;AS_VarDP=0|0|0;DP=1;FILTERED_HAPS=0;QUALapprox=40;RAW_GT_COUNT=0,0,1;RAW_MQandDP=4,1;TREE_SCORE=0.882212;VarDP=1	GT:AD:DP:GQ:PGT:PID:PL:PS:SB	1|1:0,1,0:1:3:0|1:792473_C_T:40,3,0,45,3,40:792473:0,0,1,0
+chr1	792474	.	G	<NON_REF>	.	.	END=792490	GT:DP:GQ	0/0:1:0
+chr1	792491	.	G	GA,<NON_REF>	30.44	.	ASSEMBLED_HAPS=4;AS_QUALapprox=|40|0;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|4.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|0,0|0,0;AS_VarDP=0|0|0;DP=1;FILTERED_HAPS=0;QUALapprox=40;RAW_GT_COUNT=0,0,1;RAW_MQandDP=4,1;TREE_SCORE=0.322956;VarDP=1	GT:AD:DP:GQ:PGT:PID:PL:PS:SB	1|1:0,1,0:1:3:0|1:792473_C_T:40,3,0,45,3,40:792473:0,0,1,0
+chr1	792492	.	T	<NON_REF>	.	.	END=792509	GT:DP:GQ	0/0:1:0
+chr1	792510	.	T	C,<NON_REF>	30.48	.	ASSEMBLED_HAPS=4;AS_QUALapprox=|40|0;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|4.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|0,0|0,0;AS_VarDP=0|0|0;DP=1;FILTERED_HAPS=0;QUALapprox=40;RAW_GT_COUNT=0,0,1;RAW_MQandDP=4,1;TREE_SCORE=0.761834;VarDP=1	GT:AD:DP:GQ:PGT:PID:PL:PS:SB	1|1:0,1,0:1:3:0|1:792473_C_T:40,3,0,45,3,40:792473:0,0,1,0
+chr1	792511	.	C	<NON_REF>	.	.	END=792532	GT:DP:GQ	0/0:1:0
+chr1	792533	.	A	G,<NON_REF>	30.48	.	ASSEMBLED_HAPS=4;AS_QUALapprox=|40|0;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|4.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|0,0|0,0;AS_VarDP=0|0|0;DP=1;FILTERED_HAPS=0;QUALapprox=40;RAW_GT_COUNT=0,0,1;RAW_MQandDP=4,1;TREE_SCORE=0.88142;VarDP=1	GT:AD:DP:GQ:PGT:PID:PL:PS:SB	1|1:0,1,0:1:3:0|1:792473_C_T:40,3,0,45,3,40:792473:0,0,1,0
+chr1	792534	.	C	<NON_REF>	.	.	END=853826	GT:DP:GQ	0/0:4:0
+chr1	853827	.	CGCCGTGTGGTAAACTGATGAACCCCGACCCTGATCAACATGAGATGACT	C,<NON_REF>	65.60	.	ASSEMBLED_HAPS=2;AS_QUALapprox=|73|0;AS_RAW_BaseQRankSum=|0.9,1|NaN;AS_RAW_MQ=3600.00|4292.00|0.00;AS_RAW_MQRankSum=|-1.0,1|NaN;AS_RAW_ReadPosRankSum=|0.0,1|NaN;AS_SB_TABLE=0,1|0,2|0,0;AS_VarDP=1|2|0;BaseQRankSum=0.967;DP=3;FILTERED_HAPS=0;MQRankSum=-0.967;QUALapprox=73;RAW_GT_COUNT=0,1,0;RAW_MQandDP=7892,3;ReadPosRankSum=0;TREE_SCORE=0.912092;VarDP=3	GT:AD:DP:GQ:PL:SB	0/1:1,2,0:3:36:73,0,36,84,42,117:0,1,0,2
+chr1	853877	.	G	<NON_REF>	.	.	END=854270	GT:DP:GQ	0/0:3:0
+chr1	854271	.	A	G,<NON_REF>	35.48	.	ASSEMBLED_HAPS=2;AS_QUALapprox=|45|0;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|324.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|0,0|0,0;AS_VarDP=0|0|0;DP=1;FILTERED_HAPS=0;QUALapprox=45;RAW_GT_COUNT=0,0,1;RAW_MQandDP=324,1;TREE_SCORE=0.962214;VarDP=1	GT:AD:DP:GQ:PL:SB	1/1:0,1,0:1:3:45,3,0,45,3,45:0,0,0,1
+chr1	854272	.	T	<NON_REF>	.	.	END=864082	GT:DP:GQ	0/0:0:0
+chr1	864083	.	T	C,<NON_REF>	35.48	.	ASSEMBLED_HAPS=2;AS_QUALapprox=|45|0;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|676.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|0,0|0,0;AS_VarDP=0|0|0;DP=1;FILTERED_HAPS=0;QUALapprox=45;RAW_GT_COUNT=0,0,1;RAW_MQandDP=676,1;TREE_SCORE=0.968235;VarDP=1	GT:AD:DP:GQ:PL:SB	1/1:0,1,0:1:3:45,3,0,45,3,45:0,0,0,1
+chr1	864084	.	A	<NON_REF>	.	.	END=864445	GT:DP:GQ	0/0:4:0
+chr1	864446	.	C	<NON_REF>	.	.	END=864455	GT:DP:GQ	0/0:7:20
+chr1	864456	.	T	<NON_REF>	.	.	END=864514	GT:DP:GQ	0/0:6:0
+chr1	864515	.	G	<NON_REF>	.	.	END=864524	GT:DP:GQ	0/0:7:20
+chr1	864525	.	A	<NON_REF>	.	.	END=864528	GT:DP:GQ	0/0:7:0
+chr1	864529	.	C	<NON_REF>	.	.	END=864550	GT:DP:GQ	0/0:8:20
+chr1	864551	.	A	<NON_REF>	.	.	END=864551	GT:DP:GQ	0/0:7:0
+chr1	864552	.	T	<NON_REF>	.	.	END=864575	GT:DP:GQ	0/0:7:20
+chr1	864576	.	C	<NON_REF>	.	.	END=864576	GT:DP:GQ	0/0:7:0
+chr1	864577	.	T	<NON_REF>	.	.	END=864607	GT:DP:GQ	0/0:7:20
+chr1	864608	.	C	<NON_REF>	.	.	END=864609	GT:DP:GQ	0/0:7:0
+chr1	864610	.	T	<NON_REF>	.	.	END=864626	GT:DP:GQ	0/0:7:20
+chr1	864627	.	T	C,<NON_REF>	80.02	.	ASSEMBLED_HAPS=2;AS_QUALapprox=|94|0;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|11044.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|3,4|0,0;AS_VarDP=0|7|0;DP=7;FILTERED_HAPS=0;QUALapprox=94;RAW_GT_COUNT=0,0,1;RAW_MQandDP=11044,7;TREE_SCORE=0.997055;VarDP=7	GT:AD:DP:GQ:PL:SB	1/1:0,7,0:7:21:94,21,0,315,21,94:0,0,3,4
+chr1	864628	.	T	<NON_REF>	.	.	END=864658	GT:DP:GQ	0/0:7:20
+chr1	864659	.	A	<NON_REF>	.	.	END=886481	GT:DP:GQ	0/0:4:0
+chr1	886482	.	CACAGCAGCTGTGCTGTGTT	C,<NON_REF>	67.60	.	ASSEMBLED_HAPS=54;AS_QUALapprox=|75|0;AS_RAW_BaseQRankSum=|0.0,1|NaN;AS_RAW_MQ=3600.00|10009.00|0.00;AS_RAW_MQRankSum=|-0.4,1|NaN;AS_RAW_ReadPosRankSum=|-1.2,1|NaN;AS_SB_TABLE=1,0|3,0|0,0;AS_VarDP=1|3|0;BaseQRankSum=0;DP=4;FILTERED_HAPS=43;MQRankSum=-0.319;QUALapprox=75;RAW_GT_COUNT=0,1,0;RAW_MQandDP=13609,4;ReadPosRankSum=-1.15;TREE_SCORE=0.94488;VarDP=4	GT:AD:DP:GQ:PL:SB	0/1:1,3,0:4:33:75,0,33,112,42,117:1,0,3,0
+chr1	886502	.	A	<NON_REF>	.	.	END=886506	GT:DP:GQ	0/0:4:0
+chr1	886507	.	A	G,<NON_REF>	73.13	.	ASSEMBLED_HAPS=54;AS_QUALapprox=|87|0;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|13609.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|4,0|0,0;AS_VarDP=0|4|0;DP=4;FILTERED_HAPS=43;QUALapprox=87;RAW_GT_COUNT=0,0,1;RAW_MQandDP=13609,4;TREE_SCORE=0.998201;VarDP=4	GT:AD:DP:GQ:PL:SB	1/1:0,4,0:4:12:87,12,0,166,12,87:0,0,4,0
+chr1	886508	.	A	<NON_REF>	.	.	END=886567	GT:DP:GQ	0/0:4:0
+chr1	886568	.	T	C,<NON_REF>	70.83	.	ASSEMBLED_HAPS=8;AS_QUALapprox=|84|0;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|10800.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|3,0|0,0;AS_VarDP=0|3|0;DP=3;FILTERED_HAPS=4;QUALapprox=84;RAW_GT_COUNT=0,0,1;RAW_MQandDP=10800,3;TREE_SCORE=0.998735;VarDP=3	GT:AD:DP:GQ:PL:SB	1/1:0,3,0:3:9:84,9,0,135,9,84:0,0,3,0
+chr1	886569	.	G	<NON_REF>	.	.	END=910957	GT:DP:GQ	0/0:2:0
+chr1	910958	.	A	G,<NON_REF>	69.31	.	ASSEMBLED_HAPS=29;AS_QUALapprox=|81|0;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|7200.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|0,0|0,0;AS_VarDP=0|2|0;DP=2;FILTERED_HAPS=14;QUALapprox=81;RAW_GT_COUNT=0,0,1;RAW_MQandDP=7200,2;TREE_SCORE=0.997784;VarDP=2	GT:AD:DP:GQ:PL:SB	1/1:0,2,0:2:6:81,6,0,90,6,81:0,0,0,2
+chr1	910959	.	C	<NON_REF>	.	.	END=911017	GT:DP:GQ	0/0:3:0
+chr1	911018	.	G	A,<NON_REF>	73.13	.	ASSEMBLED_HAPS=53;AS_QUALapprox=|87|0;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|14400.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|1,3|0,0;AS_VarDP=0|4|0;DP=4;FILTERED_HAPS=18;QUALapprox=87;RAW_GT_COUNT=0,0,1;RAW_MQandDP=14400,4;TREE_SCORE=0.998602;VarDP=4	GT:AD:DP:GQ:PL:SB	1/1:0,4,0:4:12:87,12,0,180,12,87:0,0,1,3
+chr1	911019	.	C	<NON_REF>	.	.	END=911084	GT:DP:GQ	0/0:5:0
+chr1	911085	.	C	T,CTG,<NON_REF>	85.05	.	ASSEMBLED_HAPS=92;AS_QUALapprox=|72|30|0;AS_RAW_BaseQRankSum=|0.0,1|0.6,1|NaN;AS_RAW_MQ=3600.00|7200.00|3600.00|0.00;AS_RAW_MQRankSum=|0.0,1|0.0,1|NaN;AS_RAW_ReadPosRankSum=|0.0,1|0.6,1|NaN;AS_SB_TABLE=1,0|0,2|0,1|0,0;AS_VarDP=1|2|1|0;BaseQRankSum=0.319;DP=5;FILTERED_HAPS=66;MQRankSum=0;QUALapprox=102;RAW_GT_COUNT=0,0,1;RAW_MQandDP=18000,5;ReadPosRankSum=0.319;TREE_SCORE=0.997046;VarDP=4	GT:AD:DP:GQ:PL:SB	1/2:1,2,1,0:4:30:102,30,36,72,0,75,114,42,84,117:1,0,0,3
+chr1	911086	.	C	<NON_REF>	.	.	END=911162	GT:DP:GQ	0/0:4:0
+chr1	911163	.	G	T,<NON_REF>	64.74	.	ASSEMBLED_HAPS=92;AS_QUALapprox=|72|0;AS_RAW_BaseQRankSum=|0.9,1|NaN;AS_RAW_MQ=3600.00|7200.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|0.0,1|NaN;AS_SB_TABLE=1,0|0,2|0,0;AS_VarDP=1|2|0;BaseQRankSum=0.967;DP=4;FILTERED_HAPS=66;MQRankSum=0;QUALapprox=72;RAW_GT_COUNT=0,1,0;RAW_MQandDP=14400,4;ReadPosRankSum=0;TREE_SCORE=0.997113;VarDP=3	GT:AD:DP:GQ:PL:SB	0/1:1,2,0:3:6:72,0,6,84,12,87:1,0,0,2
+chr1	911164	.	C	<NON_REF>	.	.	END=911219	GT:DP:GQ	0/0:5:0
+chr1	911220	.	CT	C,<NON_REF>	75.92	.	ASSEMBLED_HAPS=92;AS_QUALapprox=|90|0;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|18000.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|3,2|0,0;AS_VarDP=0|5|0;DP=6;FILTERED_HAPS=66;QUALapprox=90;RAW_GT_COUNT=0,0,1;RAW_MQandDP=21600,6;TREE_SCORE=0.939408;VarDP=5	GT:AD:DP:GQ:PL:SB	1/1:0,5,0:5:15:90,15,0,150,15,90:0,0,3,2
+chr1	911222	.	T	<NON_REF>	.	.	END=911427	GT:DP:GQ	0/0:6:0
+chr1	911428	.	C	T,<NON_REF>	70.83	.	ASSEMBLED_HAPS=16;AS_QUALapprox=|84|0;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|10800.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|2,1|0,0;AS_VarDP=0|3|0;DP=3;FILTERED_HAPS=0;QUALapprox=84;RAW_GT_COUNT=0,0,1;RAW_MQandDP=10800,3;TREE_SCORE=0.998747;VarDP=3	GT:AD:DP:GQ:PL:SB	1/1:0,3,0:3:9:84,9,0,135,9,84:0,0,2,1
+chr1	911429	.	G	<NON_REF>	.	.	END=911483	GT:DP:GQ	0/0:3:0
+chr1	911484	.	G	C,<NON_REF>	69.31	.	ASSEMBLED_HAPS=16;AS_QUALapprox=|81|0;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|7200.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|0,0|0,0;AS_VarDP=0|2|0;DP=2;FILTERED_HAPS=0;QUALapprox=81;RAW_GT_COUNT=0,0,1;RAW_MQandDP=7200,2;TREE_SCORE=0.997889;VarDP=2	GT:AD:DP:GQ:PL:SB	1/1:0,2,0:2:6:81,6,0,90,6,81:0,0,1,1
+chr1	911485	.	A	<NON_REF>	.	.	END=911488	GT:DP:GQ	0/0:2:0
+chr1	911489	.	G	GA,<NON_REF>	35.44	.	ASSEMBLED_HAPS=16;AS_QUALapprox=|45|0;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|3600.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|0,0|0,0;AS_VarDP=0|0|0;DP=2;FILTERED_HAPS=0;QUALapprox=45;RAW_GT_COUNT=0,0,1;RAW_MQandDP=7200,2;TREE_SCORE=0.401004;VarDP=1	GT:AD:DP:GQ:PGT:PID:PL:PS:SB	1|1:0,1,0:1:3:0|1:911489_G_GA:45,3,0,45,3,45:911489:0,0,1,0
+chr1	911490	.	T	<NON_REF>	.	.	END=911495	GT:DP:GQ	0/0:1:0
+chr1	911496	.	TG	T,<NON_REF>	35.44	.	ASSEMBLED_HAPS=16;AS_QUALapprox=|45|0;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|3600.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|0,0|0,0;AS_VarDP=0|0|0;DP=1;FILTERED_HAPS=0;QUALapprox=45;RAW_GT_COUNT=0,0,1;RAW_MQandDP=3600,1;TREE_SCORE=0.288179;VarDP=1	GT:AD:DP:GQ:PGT:PID:PL:PS:SB	1|1:0,1,0:1:3:0|1:911489_G_GA:45,3,0,45,3,45:911489:0,0,1,0
+chr1	911498	.	G	<NON_REF>	.	.	END=918107	GT:DP:GQ	0/0:0:0
+chr1	918108	.	G	A,<NON_REF>	35.48	.	ASSEMBLED_HAPS=2;AS_QUALapprox=|45|0;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|3600.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|0,0|0,0;AS_VarDP=0|0|0;DP=1;FILTERED_HAPS=0;QUALapprox=45;RAW_GT_COUNT=0,0,1;RAW_MQandDP=3600,1;TREE_SCORE=0.984729;VarDP=1	GT:AD:DP:GQ:PL:SB	1/1:0,1,0:1:3:45,3,0,45,3,45:0,0,1,0
+chr1	918109	.	G	<NON_REF>	.	.	END=918787	GT:DP:GQ	0/0:3:0
+chr1	918788	.	C	T,<NON_REF>	35.48	.	ASSEMBLED_HAPS=2;AS_QUALapprox=|45|0;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|3600.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|0,0|0,0;AS_VarDP=0|0|0;DP=1;FILTERED_HAPS=0;QUALapprox=45;RAW_GT_COUNT=0,0,1;RAW_MQandDP=3600,1;TREE_SCORE=0.984121;VarDP=1	GT:AD:DP:GQ:PL:SB	1/1:0,1,0:1:3:45,3,0,45,3,45:0,0,1,0
+chr1	918789	.	A	<NON_REF>	.	.	END=922447	GT:DP:GQ	0/0:0:0
+chr1	922448	.	A	G,<NON_REF>	66.64	.	ASSEMBLED_HAPS=8;AS_QUALapprox=|74|0;AS_RAW_BaseQRankSum=|-0.5,1|NaN;AS_RAW_MQ=3600.00|7200.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|-1.0,1|NaN;AS_SB_TABLE=0,1|1,1|0,0;AS_VarDP=1|2|0;BaseQRankSum=-0.431;DP=3;FILTERED_HAPS=4;MQRankSum=0;QUALapprox=74;RAW_GT_COUNT=0,1,0;RAW_MQandDP=10800,3;ReadPosRankSum=-0.967;TREE_SCORE=0.998515;VarDP=3	GT:AD:DP:GQ:PL:SB	0/1:1,2,0:3:36:74,0,36,77,42,117:0,1,1,1
+chr1	922449	.	G	<NON_REF>	.	.	END=922672	GT:DP:GQ	0/0:5:0
+chr1	922673	.	T	<NON_REF>	.	.	END=922678	GT:DP:GQ	0/0:7:20
+chr1	922679	.	G	<NON_REF>	.	.	END=922679	GT:DP:GQ	0/0:6:0
+chr1	922680	.	A	<NON_REF>	.	.	END=922680	GT:DP:GQ	0/0:7:20
+chr1	922681	.	G	<NON_REF>	.	.	END=922681	GT:DP:GQ	0/0:6:0
+chr1	922682	.	C	<NON_REF>	.	.	END=922684	GT:DP:GQ	0/0:7:20
+chr1	922685	.	T	<NON_REF>	.	.	END=922686	GT:DP:GQ	0/0:7:0
+chr1	922687	.	C	<NON_REF>	.	.	END=922690	GT:DP:GQ	0/0:7:20
+chr1	922691	.	C	<NON_REF>	.	.	END=922701	GT:DP:GQ	0/0:7:0
+chr1	922702	.	C	<NON_REF>	.	.	END=922711	GT:DP:GQ	0/0:7:20
+chr1	922712	.	T	<NON_REF>	.	.	END=950541	GT:DP:GQ	0/0:4:0
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/expected.NA12878.rb.g.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/expected.NA12878.rb.g.vcf.idx
new file mode 100644
index 00000000000..cf9d16e7f1d
Binary files /dev/null and b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/expected.NA12878.rb.g.vcf.idx differ
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/expected.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/expected.vcf
new file mode 100644
index 00000000000..f8814112e3f
--- /dev/null
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/expected.vcf
@@ -0,0 +1,3468 @@
+##fileformat=VCFv4.2
+##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
+##FILTER=<ID=ExcessHet,Description="ExcessHet > 54.69">
+##FILTER=<ID=LowQual,Description="Low quality">
+##FILTER=<ID=PASS,Description="All filters passed">
+##FILTER=<ID=VQSRTrancheINDEL95.00to96.00,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -0.6569 <= x < 0.279">
+##FILTER=<ID=VQSRTrancheINDEL96.00to97.00,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -1.6439 <= x < -0.6569">
+##FILTER=<ID=VQSRTrancheINDEL97.00to99.00,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -2.2703 <= x < -1.6439">
+##FILTER=<ID=VQSRTrancheINDEL99.00to99.50,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -2.8149 <= x < -2.2703">
+##FILTER=<ID=VQSRTrancheINDEL99.50to99.90,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -8.5966 <= x < -2.8149">
+##FILTER=<ID=VQSRTrancheINDEL99.90to99.95,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -17.5558 <= x < -8.5966">
+##FILTER=<ID=VQSRTrancheINDEL99.95to100.00+,Description="Truth sensitivity tranche level for INDEL model at VQS Lod < -29637.063">
+##FILTER=<ID=VQSRTrancheINDEL99.95to100.00,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -29637.063 <= x < -17.5558">
+##FILTER=<ID=VQSRTrancheSNP99.90to100.00+,Description="Truth sensitivity tranche level for SNP model at VQS Lod < -10.0">
+##FILTER=<ID=VQSRTrancheSNP99.90to100.00,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -10.0 <= x < -9.6">
+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
+##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">
+##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
+##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
+##GATKCommandLine=<ID=ApplyVQSR,CommandLine="ApplyVQSR --recal-file /cromwell_root/broad-gotc-dev-cromwell-execution/TestJointGenotyping/a3ff7861-f2c1-4203-901c-9c9b614c672d/call-JointGenotyping/JointGenotyping/d91d9f8c-b2c4-4260-8cb1-e0347c5159e8/call-IndelsVariantRecalibrator/small_callset_low_threshold.indels.recal --tranches-file /cromwell_root/broad-gotc-dev-cromwell-execution/TestJointGenotyping/a3ff7861-f2c1-4203-901c-9c9b614c672d/call-JointGenotyping/JointGenotyping/d91d9f8c-b2c4-4260-8cb1-e0347c5159e8/call-IndelsVariantRecalibrator/small_callset_low_threshold.indels.tranches --output tmp.indel.recalibrated.vcf --truth-sensitivity-filter-level 95.0 --use-allele-specific-annotations true --mode INDEL --variant /cromwell_root/broad-gotc-dev-cromwell-execution/TestJointGenotyping/a3ff7861-f2c1-4203-901c-9c9b614c672d/call-JointGenotyping/JointGenotyping/d91d9f8c-b2c4-4260-8cb1-e0347c5159e8/call-HardFilterAndMakeSitesOnlyVcf/shard-0/small_callset_low_threshold.0.variant_filtered.vcf.gz --create-output-variant-index true --ignore-all-filters false --exclude-filtered false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false",Version="4.5.0.0",Date="February 10, 2024 at 5:31:35 AM GMT">
+##GATKCommandLine=<ID=SelectVariants,CommandLine="SelectVariants --output /Users/mshand/Github/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/expected.vcf --variant expected_small_no_nocalls.vcf.gz --intervals chr1:1-945670 --apply-jexl-filters-first false --invertSelect false --exclude-non-variants false --exclude-filtered false --preserve-alleles false --remove-unused-alternates false --restrict-alleles-to ALL --keep-original-ac false --keep-original-dp false --mendelian-violation false --invert-mendelian-violation false --mendelian-violation-qual-threshold 0.0 --select-random-fraction 1.0 --remove-fraction-genotypes 0.0 --ignore-non-ref-in-types false --fully-decode false --max-indel-size 2147483647 --min-indel-size 0 --max-filtered-genotypes 2147483647 --min-filtered-genotypes 0 --max-fraction-filtered-genotypes 1.0 --min-fraction-filtered-genotypes 0.0 --max-nocall-number 2147483647 --max-nocall-fraction 1.0 --set-filtered-gt-to-nocall false --allow-nonoverlapping-command-line-samples false --suppress-reference-path false --fail-on-unsorted-genotype false --genomicsdb-max-alternate-alleles 50 --call-genotypes false --genomicsdb-use-bcf-codec false --genomicsdb-shared-posixfs-optimizations false --genomicsdb-use-gcs-hdfs-connector false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false",Version="4.6.0.0-19-g6a6872f-SNAPSHOT",Date="July 30, 2024 at 4:29:02 PM EDT">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=AS_BaseQRankSum,Number=A,Type=Float,Description="allele specific Z-score from Wilcoxon rank sum test of each Alt Vs. Ref base qualities">
+##INFO=<ID=AS_FS,Number=A,Type=Float,Description="allele specific phred-scaled p-value using Fisher's exact test to detect strand bias of each alt allele">
+##INFO=<ID=AS_FilterStatus,Number=A,Type=String,Description="Filter status for each allele, as assessed by ApplyVQSR. Note that the VCF filter field will reflect the most lenient/sensitive status across all alleles.">
+##INFO=<ID=AS_InbreedingCoeff,Number=A,Type=Float,Description="Allele-specific inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
+##INFO=<ID=AS_MQ,Number=A,Type=Float,Description="Allele-specific RMS Mapping Quality">
+##INFO=<ID=AS_MQRankSum,Number=A,Type=Float,Description="Allele-specific Mapping Quality Rank Sum">
+##INFO=<ID=AS_QD,Number=A,Type=Float,Description="Allele-specific Variant Confidence/Quality by Depth">
+##INFO=<ID=AS_QUALapprox,Number=1,Type=String,Description="Allele-specific QUAL approximations">
+##INFO=<ID=AS_RAW_BaseQRankSum,Number=1,Type=String,Description="raw data for allele specific rank sum test of base qualities">
+##INFO=<ID=AS_RAW_MQ,Number=1,Type=String,Description="Allele-specfic raw data for RMS Mapping Quality">
+##INFO=<ID=AS_RAW_MQRankSum,Number=1,Type=String,Description="Allele-specfic raw data for Mapping Quality Rank Sum">
+##INFO=<ID=AS_RAW_ReadPosRankSum,Number=1,Type=String,Description="allele specific raw data for rank sum test of read position bias">
+##INFO=<ID=AS_ReadPosRankSum,Number=A,Type=Float,Description="allele specific Z-score from Wilcoxon rank sum test of each Alt vs. Ref read position bias">
+##INFO=<ID=AS_SB_TABLE,Number=1,Type=String,Description="Allele-specific forward/reverse read counts for strand bias tests">
+##INFO=<ID=AS_SOR,Number=A,Type=Float,Description="Allele specific strand Odds Ratio of 2x|Alts| contingency table to detect allele specific strand bias">
+##INFO=<ID=AS_VQSLOD,Number=A,Type=String,Description="For each alt allele, the log odds of being a true variant versus being false under the trained gaussian mixture model">
+##INFO=<ID=AS_VarDP,Number=1,Type=String,Description="Allele-specific (informative) depth over variant genotypes; effectively sum of ADs">
+##INFO=<ID=AS_culprit,Number=A,Type=String,Description="For each alt allele, the annotation which was the worst performing in the Gaussian mixture model, likely the reason why the variant was filtered out">
+##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
+##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
+##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
+##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
+##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
+##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
+##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
+##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
+##INFO=<ID=MQ_DP,Number=1,Type=Integer,Description="Depth over variant samples for better MQ calculation (deprecated -- use RAW_MQandDP instead.">
+##INFO=<ID=NEGATIVE_TRAIN_SITE,Number=0,Type=Flag,Description="This variant was used to build the negative training set of bad variants">
+##INFO=<ID=POSITIVE_TRAIN_SITE,Number=0,Type=Flag,Description="This variant was used to build the positive training set of good variants">
+##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
+##INFO=<ID=QUALapprox,Number=1,Type=Integer,Description="Sum of PL[0] values; used to approximate the QUAL score">
+##INFO=<ID=RAW_GT_COUNT,Number=3,Type=Integer,Description="Counts of genotypes w.r.t. the reference allele: 0/0, 0/*, */*, i.e. all alts lumped together; for use in calculating excess heterozygosity">
+##INFO=<ID=RAW_MQandDP,Number=2,Type=Integer,Description="Raw data (sum of squared MQ and total depth) for improved RMS Mapping Quality calculation. Incompatible with deprecated RAW_MQ formulation.">
+##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
+##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
+##INFO=<ID=VQSLOD,Number=1,Type=Float,Description="Log odds of being a true variant versus being false under the trained gaussian mixture model">
+##INFO=<ID=VarDP,Number=1,Type=Integer,Description="(informative) depth over variant genotypes">
+##INFO=<ID=culprit,Number=1,Type=String,Description="The annotation which was the worst performing in the Gaussian mixture model, likely the reason why the variant was filtered out">
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+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	CHMI_CHMI3_Nex1	NA12878	NA12891	NA12892	NA19238	NA20845	NA20846	NA20847	NA20849	NA20850	NA20851	NA20852	NA20853	NA20854	NA20856	NA20858	NA20859	NA20861	NA20862	NA20866	NA20869	NA20870	NA20871	NA20872	NA20873	NA20874	NA20875	NA20876	NA20877	NA20878	NA20881	NA20885	NA20886	NA20887	NA20888	NA20889	NA20890	NA20891	NA20892	NA20893	NA20894	NA20895	NA20896	NA20897	NA20898	NA20899	NA20901	NA20902	NA20903	NA20904	NA20905	NA20906	NA20908	NA20910	NA20911	NA21086	NA21087	NA21088	NA21093	NA21095	NA21114	NA21124	NA21126	NA21129	NA21137
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+chr1	187471	.	A	C	60.64	VQSRTrancheSNP99.90to100.00+	AC=2;AF=0.015;AN=130;AS_BaseQRankSum=3.100;AS_FS=100.350;AS_FilterStatus=VQSRTrancheSNP99.90to100.00+;AS_InbreedingCoeff=-0.0159;AS_MQ=28.18;AS_MQRankSum=-3.400;AS_QD=0.13;AS_ReadPosRankSum=-5.650;AS_SOR=6.803;AS_VQSLOD=-93.9689;AS_culprit=AS_FS;BaseQRankSum=3.47;DP=2943;ExcessHet=0.0338;FS=100.350;InbreedingCoeff=-0.0159;MLEAC=1;MLEAF=7.692e-03;MQ=32.38;MQRankSum=-3.205e+00;QD=0.12;ReadPosRankSum=-4.542e+00;SOR=6.803	GT:AD:DP:GQ:PL	0/0:242,0:242:10	0/1:197,31:228:77:77,0,8939	0/1:229,29:258:12:12,0,8067	0/0:283,0:283:60	0/0:27,0:27:60	0/0:26,0:26:60	0/0:35,0:35:60	0/0:29,0:29:60	0/0:34,0:34:60	0/0:40,0:40:60	0/0:31,0:31:60	0/0:32,0:32:60	0/0:27,0:27:60	0/0:28,0:28:60	0/0:29,0:29:60	0/0:27,0:27:60	0/0:37,0:37:60	0/0:32,0:32:60	0/0:37,0:37:60	0/0:29,0:29:60	0/0:29,0:29:60	0/0:32,0:32:60	0/0:28,0:28:60	0/0:26,0:26:60	0/0:32,0:32:60	0/0:32,0:32:60	0/0:49,0:49:60	0/0:29,0:29:60	0/0:27,0:27:60	0/0:28,0:28:60	0/0:33,0:33:60	0/0:31,0:31:60	0/0:33,0:33:60	0/0:30,0:30:60	0/0:31,0:31:60	0/0:29,0:29:60	0/0:34,0:34:60	0/0:28,0:28:60	0/0:29,0:29:60	0/0:51,0:51:60	0/0:30,0:30:60	0/0:29,0:29:60	0/0:31,0:31:60	0/0:32,0:32:60	0/0:33,0:33:60	0/0:58,0:58:60	0/0:27,0:27:60	0/0:32,0:32:60	0/0:38,0:38:60	0/0:28,0:28:60	0/0:32,0:32:60	0/0:31,0:31:60	0/0:28,0:28:60	0/0:28,0:28:60	0/0:31,0:31:60	0/0:28,0:28:60	0/0:29,0:29:60	0/0:31,0:31:60	0/0:28,0:28:60	0/0:28,0:28:60	0/0:31,0:31:60	0/0:30,0:30:60	0/0:42,0:42:60	0/0:27,0:27:60	0/0:29,0:29:60
+chr1	187485	.	G	A	97359.39	ExcessHet	AC=74;AF=0.569;AN=130;AS_BaseQRankSum=0.000;AS_FS=4.039;AS_InbreedingCoeff=-0.7568;AS_MQ=29.24;AS_MQRankSum=-0.400;AS_QD=17.72;AS_ReadPosRankSum=0.050;AS_SOR=0.989;BaseQRankSum=0.058;DP=5503;ExcessHet=100.7690;FS=4.039;InbreedingCoeff=-0.7568;MLEAC=74;MLEAF=0.569;MQ=29.46;MQRankSum=-3.180e-01;QD=17.72;ReadPosRankSum=0.110;SOR=0.991	GT:AD:DP:GQ:PGT:PID:PL	0/1:33,235:271:99:.:.:7017,0,616	1/1:9,236:245:99:.:.:7627,450,0	0/1:131,138:269:99:.:.:2911,0,3374	0/1:93,207:300:99:.:.:6270,0,1857	0/1:18,53:71:99:0|1:187485_G_A:1410,0,246	0/1:18,41:59:99:0|1:187485_G_A:1145,0,299	0/1:44,46:90:99:.:.:1011,0,919	0/1:26,20:46:99:0|1:187485_G_A:598,0,582	0/1:53,49:102:99:0|1:187485_G_A:1184,0,1070	0/1:28,63:91:99:0|1:187485_G_A:2155,0,486	0/1:19,37:56:99:0|1:187485_G_A:1017,0,356	0/1:12,75:87:51:.:.:2110,0,51	0/1:32,49:81:99:0|1:187485_G_A:1489,0,616	0/1:55,35:90:99:.:.:676,0,1231	0/1:25,29:54:99:.:.:666,0,511	1/1:0,27:27:81:.:.:751,81,0	0/1:36,26:62:99:.:.:519,0,810	0/1:35,55:90:99:0|1:187485_G_A:1513,0,681	0/1:26,48:74:99:0|1:187485_G_A:1506,0,471	0/1:24,50:74:99:0|1:187485_G_A:1421,0,411	0/1:23,27:50:99:0|1:187485_G_A:822,0,471	0/1:16,63:79:99:.:.:1442,0,168	0/1:22,61:83:99:0|1:187485_G_A:2141,0,345	0/1:72,15:87:99:.:.:162,0,1680	0/1:38,34:72:99:.:.:736,0,816	0/1:37,41:78:99:0|1:187485_G_A:1062,0,750	0/1:22,70:92:99:0|1:187485_G_A:1904,0,324	0/1:26,77:103:99:0|1:187485_G_A:2415,0,387	1/1:0,31:31:93:.:.:841,93,0	0/1:25,34:59:99:.:.:710,0,515	1/1:0,51:51:99:1|1:187485_G_A:1640,153,0	0/1:43,39:82:99:.:.:806,0,923	1/1:4,57:61:84:.:.:1436,84,0	0/1:46,46:92:99:.:.:958,0,977	0/1:24,43:67:99:0|1:187485_G_A:1301,0,460	0/1:19,20:39:99:.:.:452,0,396	0/1:42,36:78:99:.:.:765,0,870	0/1:38,38:76:99:.:.:802,0,786	0/1:18,58:76:99:0|1:187485_G_A:1530,0,265	0/1:52,25:77:99:.:.:537,0,1213	0/1:39,25:64:99:0|1:187485_G_A:794,0,794	0/1:28,110:138:99:0|1:187485_G_A:3079,0,354	0/1:40,18:58:99:.:.:320,0,904	0/1:17,52:69:99:0|1:187485_G_A:1338,0,262	0/1:10,45:55:93:.:.:1053,0,93	0/1:34,41:75:99:0|1:187485_G_A:1180,0,705	1/1:0,39:39:99:1|1:187485_G_A:1489,117,0	1/1:0,33:33:99:.:.:861,99,0	0/1:13,61:74:99:0|1:187485_G_A:1602,0,131	0/1:25,46:71:99:0|1:187485_G_A:1203,0,459	0/1:26,43:69:99:0|1:187485_G_A:1472,0,494	1/1:0,89:89:99:.:.:2606,267,0	0/1:42,51:93:99:0|1:187485_G_A:1308,0,866	0/1:14,68:82:99:.:.:1692,0,134	0/1:40,48:88:99:.:.:1016,0,787	0/1:27,17:44:99:.:.:321,0,606	0/1:18,63:81:99:0|1:187485_G_A:1650,0,240	0/1:33,36:69:99:.:.:977,0,673	0/1:20,41:61:99:.:.:1034,0,336	0/1:25,22:47:99:.:.:458,0,529	0/1:24,37:61:99:.:.:807,0,473	1/1:0,39:39:99:.:.:1071,117,0	0/1:55,93:148:99:.:.:2652,0,1049	0/1:37,44:81:99:0|1:187485_G_A:1163,0,735	0/1:65,32:97:99:.:.:550,0,1508
+chr1	187499	.	A	G	296.62	VQSRTrancheSNP99.90to100.00+	AC=1;AF=7.692e-03;AN=130;AS_BaseQRankSum=1.700;AS_FS=93.945;AS_FilterStatus=VQSRTrancheSNP99.90to100.00+;AS_InbreedingCoeff=-0.0078;AS_MQ=28.65;AS_MQRankSum=0.400;AS_QD=1.03;AS_ReadPosRankSum=1.300;AS_SOR=2.365;AS_VQSLOD=-71.4761;AS_culprit=AS_FS;BaseQRankSum=1.75;DP=2977;ExcessHet=0.0000;FS=93.945;InbreedingCoeff=-0.0078;MLEAC=1;MLEAF=7.692e-03;MQ=28.19;MQRankSum=0.454;QD=1.03;ReadPosRankSum=1.37;SOR=2.365	GT:AD:DP:GQ:PL	0/1:255,32:287:99:315,0,10200	0/0:193,0:193:60	0/0:178,0:178:60	0/0:203,0:203:60	0/0:37,0:37:60	0/0:33,0:33:60	0/0:31,0:31:60	0/0:36,0:36:60	0/0:37,0:37:60	0/0:34,0:34:60	0/0:36,0:36:60	0/0:38,0:38:60	0/0:39,0:39:60	0/0:36,0:36:60	0/0:38,0:38:60	0/0:34,0:34:60	0/0:34,0:34:60	0/0:33,0:33:60	0/0:34,0:34:60	0/0:34,0:34:60	0/0:38,0:38:60	0/0:34,0:34:60	0/0:34,0:34:60	0/0:32,0:32:60	0/0:36,0:36:60	0/0:32,0:32:60	0/0:36,0:36:60	0/0:34,0:34:60	0/0:34,0:34:60	0/0:33,0:33:60	0/0:33,0:33:60	0/0:33,0:33:60	0/0:35,0:35:60	0/0:38,0:38:60	0/0:34,0:34:60	0/0:39,0:39:60	0/0:33,0:33:60	0/0:37,0:37:60	0/0:36,0:36:60	0/0:34,0:34:60	0/0:34,0:34:60	0/0:33,0:33:60	0/0:35,0:35:60	0/0:35,0:35:60	0/0:32,0:32:60	0/0:33,0:33:60	0/0:42,0:42:60	0/0:37,0:37:60	0/0:31,0:31:60	0/0:35,0:35:60	0/0:33,0:33:60	0/0:31,0:31:60	0/0:36,0:36:60	0/0:33,0:33:60	0/0:30,0:30:60	0/0:36,0:36:60	0/0:30,0:30:60	0/0:32,0:32:60	0/0:39,0:39:60	0/0:33,0:33:60	0/0:33,0:33:60	0/0:38,0:38:60	0/0:37,0:37:60	0/0:33,0:33:60	0/0:35,0:35:60
+chr1	805887	rs201849753	T	C	2153.83	PASS	AC=4;AF=0.031;AN=130;AS_BaseQRankSum=-0.550;AS_FS=2.750;AS_FilterStatus=PASS;AS_InbreedingCoeff=-0.0317;AS_MQ=29.60;AS_MQRankSum=-0.850;AS_QD=9.32;AS_ReadPosRankSum=-0.100;AS_SOR=0.919;AS_VQSLOD=-3.4483;AS_culprit=AS_MQ;BaseQRankSum=-1.950e-01;DB;DP=2215;ExcessHet=0.2060;FS=2.750;InbreedingCoeff=-0.0317;MLEAC=4;MLEAF=0.031;MQ=31.15;MQRankSum=0.211;QD=9.32;ReadPosRankSum=0.525;SOR=0.919	GT:AD:DP:GQ:PL	0/0:22,0:22:50	0/0:30,0:30:60	0/0:33,0:33:60	0/0:28,0:28:60	0/0:36,0:36:60	0/0:38,0:38:60	0/0:34,0:34:60	0/0:32,0:32:60	0/0:36,0:36:60	0/0:35,0:35:60	0/0:35,0:35:60	0/0:32,0:32:60	0/0:33,0:33:60	0/0:32,0:32:60	0/0:32,0:32:60	0/0:32,0:32:60	0/0:34,0:34:60	0/0:28,0:28:60	0/1:35,22:57:99:500,0,830	0/0:29,0:29:60	0/0:32,0:32:60	0/0:31,0:31:60	0/0:31,0:31:60	0/0:31,0:31:60	0/0:40,0:40:60	0/0:31,0:31:60	0/0:32,0:32:60	0/0:31,0:31:60	0/0:31,0:31:60	0/0:31,0:31:60	0/0:32,0:32:60	0/0:35,0:35:60	0/0:35,0:35:60	0/0:31,0:31:60	0/0:37,0:37:60	0/0:29,0:29:60	0/0:31,0:31:60	0/0:31,0:31:60	0/1:32,35:67:99:770,0,722	0/0:32,0:32:60	0/0:32,0:32:60	0/0:35,0:35:60	0/0:29,0:29:60	0/0:32,0:32:60	0/0:33,0:33:60	0/0:36,0:36:60	0/0:31,0:31:60	0/0:30,0:30:60	0/1:27,19:46:99:413,0,646	0/0:32,0:32:60	0/0:33,0:33:60	0/0:31,0:31:60	0/0:32,0:32:60	0/0:33,0:33:60	0/1:36,25:61:99:520,0,820	0/0:28,0:28:60	0/0:30,0:30:60	0/0:41,0:41:60	0/0:34,0:34:60	0/0:39,0:39:60	0/0:38,0:38:60	0/0:34,0:34:60	0/0:36,0:36:60	0/0:29,0:29:60	0/0:31,0:31:60
+chr1	873542	rs6594027	G	A	360292.25	PASS	AC=123;AF=0.946;AN=130;AS_BaseQRankSum=2.600;AS_FS=0.000;AS_FilterStatus=PASS;AS_InbreedingCoeff=-0.0569;AS_MQ=42.71;AS_MQRankSum=0.850;AS_QD=30.67;AS_ReadPosRankSum=-1.300;AS_SOR=0.875;AS_VQSLOD=1.9433;AS_culprit=AS_MQRankSum;BaseQRankSum=2.68;DB;DP=9543;ExcessHet=0.7388;FS=0.000;InbreedingCoeff=-0.0569;MLEAC=123;MLEAF=0.946;MQ=42.59;MQRankSum=1.08;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=26.61;ReadPosRankSum=-1.219e+00;SOR=0.875	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,304:304:99:.:.:11825,914,0	1/1:0,295:295:99:1|1:873542_G_A:13243,900,0	1/1:0,229:229:99:1|1:873542_G_A:9061,695,0	1/1:0,252:252:99:1|1:873542_G_A:11407,771,0	1/1:0,164:164:99:1|1:873542_G_A:5883,496,0	1/1:0,132:132:99:1|1:873542_G_A:4996,397,0	0/1:39,162:201:99:0|1:873542_G_A:6706,0,1362	1/1:0,128:128:99:.:.:4832,394,0	1/1:0,145:145:99:1|1:873542_G_A:6515,445,0	1/1:0,121:121:99:.:.:4865,370,0	1/1:0,123:123:99:1|1:873542_G_A:4718,373,0	1/1:0,160:160:99:1|1:873542_G_A:7031,485,0	1/1:0,125:125:99:.:.:4931,376,0	0/1:27,128:155:99:.:.:4576,0,306	1/1:0,143:143:99:.:.:5677,433,0	1/1:1,184:185:99:.:.:7035,559,0	1/1:0,161:161:99:1|1:873542_G_A:6171,484,0	0/1:34,163:197:99:0|1:873542_G_A:6640,0,1206	1/1:0,122:122:99:.:.:4878,376,0	1/1:0,134:134:99:1|1:873542_G_A:6156,430,0	1/1:0,131:131:99:1|1:873542_G_A:5024,397,0	1/1:0,135:135:99:.:.:5222,412,0	1/1:1,130:131:99:1|1:873542_G_A:5826,400,0	1/1:0,144:144:99:.:.:5480,436,0	1/1:1,139:140:99:.:.:4523,394,0	1/1:0,118:118:99:.:.:5406,376,0	1/1:0,150:150:99:.:.:5863,460,0	1/1:0,160:160:99:1|1:873542_G_A:7181,491,0	1/1:0,121:121:99:1|1:873542_G_A:4672,367,0	1/1:0,111:111:99:1|1:873542_G_A:5013,346,0	1/1:0,143:143:99:1|1:873542_G_A:6487,445,0	1/1:0,155:155:99:.:.:6278,478,0	1/1:0,146:146:99:.:.:4667,439,0	1/1:0,138:138:99:.:.:4412,414,0	1/1:0,117:117:99:.:.:4646,361,0	0/1:28,169:197:99:0|1:873542_G_A:6911,0,888	1/1:1,138:139:99:.:.:5153,421,0	1/1:2,117:119:99:.:.:3826,352,0	0/1:34,136:170:99:.:.:3848,0,428	1/1:0,106:106:99:.:.:3432,318,0	1/1:0,145:145:99:.:.:4595,436,0	1/1:0,139:139:99:1|1:873542_G_A:6251,427,0	1/1:0,126:126:99:.:.:4231,379,0	1/1:0,135:135:99:.:.:4336,406,0	1/1:0,133:133:99:.:.:4297,400,0	1/1:0,129:129:99:1|1:873542_G_A:4977,394,0	1/1:0,133:133:99:1|1:873542_G_A:5071,403,0	0/1:36,138:174:99:.:.:4024,0,493	1/1:1,117:118:99:.:.:4595,355,0	1/1:0,150:150:99:1|1:873542_G_A:5788,454,0	1/1:0,105:105:99:.:.:4084,322,0	1/1:0,144:144:99:1|1:873542_G_A:5583,436,0	1/1:0,139:139:99:.:.:4531,418,0	1/1:0,128:128:99:.:.:4156,385,0	1/1:0,136:136:99:.:.:5162,424,0	1/1:0,125:125:99:1|1:873542_G_A:5604,385,0	1/1:0,112:112:99:1|1:873542_G_A:4284,343,0	1/1:0,139:139:99:.:.:4576,418,0	1/1:0,105:105:99:1|1:873542_G_A:4696,322,0	1/1:0,97:97:99:.:.:3085,291,0	1/1:1,110:111:99:1|1:873542_G_A:4202,334,0	0/1:47,140:187:99:0|1:873542_G_A:5837,0,1644	1/1:0,136:136:99:.:.:4302,409,0	1/1:0,92:92:99:1|1:873542_G_A:4198,289,0	1/1:0,148:148:99:1|1:873542_G_A:5733,451,0
+chr1	873548	rs11240780	C	T	180143.50	PASS	AC=63;AF=0.485;AN=130;AS_BaseQRankSum=0.000;AS_FS=0.000;AS_FilterStatus=PASS;AS_InbreedingCoeff=-0.0779;AS_MQ=45.20;AS_MQRankSum=0.100;AS_QD=23.59;AS_ReadPosRankSum=-0.200;AS_SOR=0.663;AS_VQSLOD=2.8579;AS_culprit=AS_MQ;BaseQRankSum=0.059;DB;DP=8868;ExcessHet=4.2585;FS=0.000;InbreedingCoeff=-0.0779;MLEAC=63;MLEAF=0.485;MQ=44.97;MQRankSum=0.142;POSITIVE_TRAIN_SITE;QD=23.59;ReadPosRankSum=-1.070e-01;SOR=0.663	GT:AD:DP:GQ:PGT:PID:PL	0/1:155,150:305:99:.:.:4084,0,4165	1/1:0,293:293:99:1|1:873542_G_A:13081,888,0	0/1:115,124:239:99:0|1:873542_G_A:3315,0,3009	1/1:0,259:259:99:1|1:873542_G_A:11566,786,0	0/1:77,86:163:99:0|1:873542_G_A:1719,0,1472	0/1:82,65:147:99:0|1:873542_G_A:1554,0,2136	0/1:38,181:219:99:0|1:873542_G_A:7109,0,1269	0/1:70,66:136:99:.:.:1675,0,1719	1/1:0,150:150:99:1|1:873542_G_A:6630,460,0	0/1:53,78:131:99:.:.:2008,0,1263	0/1:74,57:131:99:0|1:873542_G_A:1524,0,1882	1/1:0,152:152:99:1|1:873542_G_A:6839,467,0	0/1:59,70:129:99:.:.:1778,0,1540	0/1:84,74:158:99:.:.:1734,0,2852	0/1:67,85:152:99:.:.:2241,0,1738	0/1:105,92:197:99:.:.:2277,0,2734	0/1:76,84:160:99:0|1:873542_G_A:2155,0,1890	0/1:33,161:194:99:0|1:873542_G_A:6630,0,1185	0/1:58,72:130:99:.:.:1878,0,1508	1/1:0,138:138:99:1|1:873542_G_A:6127,427,0	0/1:69,61:130:99:0|1:873542_G_A:1516,0,1871	0/1:75,68:143:99:.:.:1703,0,1938	1/1:1,139:140:99:1|1:873542_G_A:6079,424,0	0/1:83,70:153:99:.:.:1765,0,2124	0/0:35,0:35:60	1/1:2,124:126:99:.:.:3889,350,0	0/1:76,80:156:99:.:.:2000,0,1996	1/1:0,162:162:99:1|1:873542_G_A:7230,497,0	0/1:64,62:126:99:0|1:873542_G_A:1656,0,1549	1/1:0,109:109:99:1|1:873542_G_A:4850,334,0	1/1:0,152:152:99:1|1:873542_G_A:6644,463,0	0/1:64,99:163:99:.:.:2656,0,1546	0/0:156,0:156:60	0/0:144,0:144:60	0/1:69,62:131:99:.:.:1645,0,1828	0/1:26,165:191:99:0|1:873542_G_A:6858,0,847	0/1:87,58:145:99:.:.:1424,0,2266	0/0:107,0:107:60	0/0:62,0:62:60	0/0:38,0:38:60	0/0:37,0:37:60	1/1:0,143:143:99:1|1:873542_G_A:6398,442,0	0/0:142,0:142:60	0/0:37,0:37:60	0/0:38,0:38:60	0/1:72,71:143:99:0|1:873542_G_A:1789,0,1854	0/1:73,64:137:99:0|1:873542_G_A:1596,0,1873	0/0:79,0:79:60	0/1:54,69:123:99:.:.:1810,0,1357	0/1:76,79:155:99:0|1:873542_G_A:1987,0,2008	0/1:52,56:108:99:.:.:1434,0,1365	0/1:70,79:149:99:0|1:873542_G_A:2086,0,1760	0/0:35,0:35:60	0/0:36,0:36:60	0/1:77,63:140:99:.:.:1583,0,1930	1/1:0,129:129:99:1|1:873542_G_A:5699,394,0	0/1:68,52:120:99:0|1:873542_G_A:1295,0,1790	0/0:123,0:123:60	1/1:0,105:105:99:1|1:873542_G_A:4740,325,0	0/0:41,0:41:60	0/1:64,57:121:99:0|1:873542_G_A:1422,0,1602	0/1:45,156:201:99:0|1:873542_G_A:6061,0,1556	0/0:107,0:107:60	1/1:0,96:96:99:1|1:873542_G_A:4197,289,0	0/1:75,81:156:99:0|1:873542_G_A:2157,0,1887
+chr1	873857	rs200657693	C	G	874.77	PASS	AC=7;AF=0.054;AN=130;AS_BaseQRankSum=0.000;AS_FS=0.851;AS_FilterStatus=PASS;AS_InbreedingCoeff=-0.0550;AS_MQ=24.53;AS_MQRankSum=-3.900;AS_QD=0.94;AS_ReadPosRankSum=-0.100;AS_SOR=0.828;AS_VQSLOD=-5.3836;AS_culprit=AS_MQ;BaseQRankSum=0.079;DB;DP=4413;ExcessHet=0.7388;FS=0.851;InbreedingCoeff=-0.0550;MLEAC=6;MLEAF=0.046;MQ=33.43;MQRankSum=-3.895e+00;QD=0.94;ReadPosRankSum=-4.400e-02;SOR=0.828	GT:AD:DP:GQ:PL	0/0:37,0:37:60	0/0:36,0:36:60	0/0:32,0:32:60	0/0:31,0:31:60	0/0:119,0:119:60	0/0:34,0:34:60	0/0:99,0:99:60	0/0:37,0:37:60	0/1:115,19:134:99:149,0,3175	0/0:34,0:34:60	0/0:137,0:137:60	0/0:35,0:35:60	0/1:104,15:119:17:17,0,2931	0/0:41,0:41:60	0/0:41,0:41:60	0/0:35,0:35:60	0/0:37,0:37:60	0/0:61,0:61:60	0/0:38,0:38:60	0/0:145,0:145:60	0/0:114,0:114:60	0/1:107,22:129:99:182,0,2959	0/0:32,0:32:60	0/0:36,0:36:60	0/0:35,0:35:60	0/0:37,0:37:60	0/0:75,0:75:60	0/1:105,26:131:99:312,0,2985	0/0:110,0:110:60	0/0:32,0:32:60	0/0:37,0:37:60	0/0:36,0:36:60	0/0:156,0:156:60	0/0:144,0:144:60	0/0:43,0:43:60	0/0:40,0:40:60	0/0:42,0:42:60	0/0:41,0:41:60	0/0:62,0:62:60	0/0:38,0:38:60	0/0:37,0:37:60	0/0:36,0:36:60	0/0:132,0:132:60	0/0:37,0:37:60	0/0:38,0:38:60	0/0:109,0:109:60	0/0:89,0:89:60	0/0:37,0:37:60	0/0:118,0:118:60	0/0:40,0:40:60	0/0:45,0:45:60	0/0:37,0:37:60	0/0:35,0:35:60	0/0:36,0:36:60	0/0:34,0:34:60	0/1:107,20:127:99:189,0,2965	0/0:39,0:39:60	0/1:153,20:173:6:6,0,4170	0/0:34,0:34:60	0/0:41,0:41:60	0/1:101,16:117:86:86,0,2791	0/0:83,0:83:60	0/0:107,0:107:60	0/0:42,0:42:60	0/0:138,0:138:60
+chr1	873921	.	C	T	316.29	VQSRTrancheSNP99.90to100.00+	AC=3;AF=0.023;AN=130;AS_BaseQRankSum=1.300;AS_FS=52.348;AS_FilterStatus=VQSRTrancheSNP99.90to100.00+;AS_InbreedingCoeff=-0.0237;AS_MQ=33.06;AS_MQRankSum=-1.800;AS_QD=0.70;AS_ReadPosRankSum=0.700;AS_SOR=7.505;AS_VQSLOD=-31.1828;AS_culprit=AS_FS;BaseQRankSum=1.37;DP=3803;ExcessHet=0.1022;FS=52.348;InbreedingCoeff=-0.0237;MLEAC=3;MLEAF=0.023;MQ=35.04;MQRankSum=-1.751e+00;QD=0.70;ReadPosRankSum=0.784;SOR=7.505	GT:AD:DP:GQ:PL	0/0:37,0:37:60	0/0:36,0:36:60	0/0:32,0:32:60	0/0:31,0:31:60	0/0:68,0:68:60	0/0:34,0:34:60	0/0:99,0:99:60	0/0:37,0:37:60	0/1:150,20:170:99:134,0,4252	0/0:34,0:34:60	0/0:33,0:33:60	0/0:35,0:35:60	0/0:38,0:38:60	0/0:41,0:41:60	0/0:41,0:41:60	0/0:35,0:35:60	0/0:37,0:37:60	0/0:61,0:61:60	0/0:38,0:38:60	0/0:145,0:145:60	0/0:137,0:137:20	0/0:34,0:34:60	0/0:32,0:32:60	0/0:36,0:36:60	0/0:35,0:35:60	0/0:37,0:37:60	0/0:75,0:75:60	0/0:37,0:37:60	0/1:126,18:144:84:84,0,3713	0/0:32,0:32:60	0/0:37,0:37:60	0/0:36,0:36:60	0/0:156,0:156:60	0/0:144,0:144:60	0/0:43,0:43:60	0/0:40,0:40:60	0/0:42,0:42:60	0/0:41,0:41:60	0/0:62,0:62:60	0/0:38,0:38:60	0/0:37,0:37:60	0/0:36,0:36:60	0/0:132,0:132:60	0/0:37,0:37:60	0/0:38,0:38:60	0/1:120,17:137:99:139,0,3406	0/0:89,0:89:60	0/0:37,0:37:60	0/0:118,0:118:60	0/0:40,0:40:60	0/0:45,0:45:60	0/0:37,0:37:60	0/0:35,0:35:60	0/0:36,0:36:60	0/0:34,0:34:60	0/0:37,0:37:60	0/0:39,0:39:60	0/0:38,0:38:60	0/0:34,0:34:60	0/0:41,0:41:60	0/0:35,0:35:60	0/0:83,0:83:60	0/0:107,0:107:60	0/0:42,0:42:60	0/0:138,0:138:60
+chr1	874460	.	C	A	804.62	PASS	AC=1;AF=7.692e-03;AN=130;AS_BaseQRankSum=0.000;AS_FS=0.000;AS_FilterStatus=PASS;AS_InbreedingCoeff=-0.0078;AS_MQ=60.00;AS_MQRankSum=0.000;AS_QD=16.10;AS_ReadPosRankSum=1.500;AS_SOR=0.952;AS_VQSLOD=5.5645;AS_culprit=AS_MQ;BaseQRankSum=0.00;DP=2844;ExcessHet=0.0000;FS=0.000;InbreedingCoeff=-0.0078;MLEAC=1;MLEAF=7.692e-03;MQ=60.00;MQRankSum=0.00;QD=16.09;ReadPosRankSum=1.60;SOR=0.952	GT:AD:DP:GQ:PL	0/0:37,0:37:60	0/0:36,0:36:60	0/0:32,0:32:60	0/0:31,0:31:60	0/0:68,0:68:60	0/0:34,0:34:60	0/0:99,0:99:60	0/0:37,0:37:60	0/0:170,0:170:60	0/0:34,0:34:60	0/0:33,0:33:60	0/0:35,0:35:60	0/0:38,0:38:60	0/0:41,0:41:60	0/0:41,0:41:60	0/0:35,0:35:60	0/0:37,0:37:60	0/0:61,0:61:60	0/0:38,0:38:60	0/0:35,0:35:60	0/0:35,0:35:60	0/0:34,0:34:60	0/0:32,0:32:60	0/0:36,0:36:60	0/0:35,0:35:60	0/0:37,0:37:60	0/0:75,0:75:60	0/0:37,0:37:60	0/0:34,0:34:60	0/0:32,0:32:60	0/0:37,0:37:60	0/0:36,0:36:60	0/0:156,0:156:60	0/1:22,28:50:99:823,0,614	0/0:43,0:43:60	0/0:40,0:40:60	0/0:42,0:42:60	0/0:41,0:41:60	0/0:62,0:62:60	0/0:38,0:38:60	0/0:37,0:37:60	0/0:36,0:36:60	0/0:34,0:34:60	0/0:37,0:37:60	0/0:38,0:38:60	0/0:41,0:41:60	0/0:89,0:89:60	0/0:37,0:37:60	0/0:35,0:35:60	0/0:40,0:40:60	0/0:45,0:45:60	0/0:37,0:37:60	0/0:35,0:35:60	0/0:36,0:36:60	0/0:34,0:34:60	0/0:37,0:37:60	0/0:39,0:39:60	0/0:38,0:38:60	0/0:34,0:34:60	0/0:41,0:41:60	0/0:35,0:35:60	0/0:23,0:23:60	0/0:31,0:31:50	0/0:16,0:16:30	0/0:35,0:35:60
+chr1	930939	rs9988021	G	A	67117.32	PASS	AC=129;AF=0.992;AN=130;AS_BaseQRankSum=0.500;AS_FS=0.000;AS_FilterStatus=PASS;AS_InbreedingCoeff=-0.0078;AS_MQ=60.00;AS_MQRankSum=0.000;AS_QD=34.24;AS_ReadPosRankSum=0.800;AS_SOR=6.051;AS_VQSLOD=4.7608;AS_culprit=AS_MQ;BaseQRankSum=0.501;DB;DP=1968;ExcessHet=0.0000;FS=0.000;InbreedingCoeff=-0.0078;MLEAC=129;MLEAF=0.992;MQ=60.00;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=34.24;ReadPosRankSum=0.843;SOR=6.051	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,56:56:99:.:.:1870,168,0	1/1:0,42:42:99:.:.:1419,126,0	1/1:0,42:42:99:.:.:1400,126,0	1/1:0,48:48:99:.:.:1528,144,0	0/1:18,17:35:99:.:.:406,0,380	1/1:0,29:29:87:.:.:1007,87,0	1/1:0,30:30:90:.:.:986,90,0	1/1:0,31:31:93:.:.:1037,93,0	1/1:0,23:23:69:.:.:798,69,0	1/1:0,21:21:63:.:.:730,63,0	1/1:0,37:37:99:.:.:1251,111,0	1/1:0,23:23:69:.:.:777,69,0	1/1:0,16:16:48:.:.:546,48,0	1/1:0,32:32:96:.:.:1101,96,0	1/1:0,43:43:99:.:.:1474,129,0	1/1:0,35:35:99:.:.:1184,105,0	1/1:0,30:30:90:.:.:1021,90,0	1/1:0,28:28:84:.:.:973,84,0	1/1:0,25:25:75:.:.:848,75,0	1/1:0,35:35:99:.:.:1161,105,0	1/1:0,38:38:99:.:.:1259,113,0	1/1:0,25:25:75:.:.:849,75,0	1/1:0,27:27:81:.:.:898,81,0	1/1:0,28:28:84:.:.:973,84,0	1/1:0,39:39:99:.:.:1326,117,0	1/1:0,28:28:84:.:.:942,84,0	1/1:0,33:33:99:.:.:1145,99,0	1/1:0,32:32:96:.:.:1082,96,0	1/1:0,33:33:99:.:.:1087,99,0	1/1:0,33:33:99:.:.:1137,99,0	1/1:0,29:29:87:.:.:1008,87,0	1/1:0,17:17:51:.:.:580,51,0	1/1:0,20:20:60:.:.:674,60,0	1/1:0,32:32:96:.:.:1065,96,0	1/1:0,25:25:75:.:.:857,75,0	1/1:0,32:32:96:.:.:1071,96,0	1/1:0,23:23:69:.:.:788,69,0	1/1:0,23:23:69:.:.:769,69,0	1/1:0,43:43:99:.:.:1485,129,0	1/1:0,25:25:75:.:.:844,75,0	1/1:0,28:28:84:.:.:926,84,0	1/1:0,28:28:84:.:.:948,84,0	1/1:0,33:33:99:.:.:1145,99,0	1/1:0,43:43:99:.:.:1453,129,0	1/1:0,20:20:60:.:.:694,60,0	1/1:0,30:30:90:.:.:1002,90,0	1/1:0,38:38:99:.:.:1320,114,0	1/1:0,29:29:87:.:.:1006,87,0	1/1:0,17:17:51:.:.:590,51,0	1/1:0,31:31:93:.:.:1056,93,0	1/1:0,29:29:87:.:.:1006,87,0	1/1:0,36:36:99:.:.:1220,108,0	1/1:0,23:23:69:.:.:767,69,0	1/1:0,31:31:93:.:.:1057,93,0	1/1:0,31:31:93:.:.:1051,93,0	1/1:0,25:25:75:.:.:844,75,0	1/1:0,20:20:60:.:.:685,60,0	1/1:0,35:35:99:.:.:1170,105,0	1/1:0,27:27:81:.:.:929,81,0	1/1:0,28:28:84:.:.:973,84,0	1/1:0,29:29:87:.:.:988,87,0	1/1:0,26:26:78:1|1:930937_G_A:903,78,0	1/1:0,32:32:96:.:.:1092,96,0	1/1:0,25:25:75:.:.:859,75,0	1/1:0,20:20:60:.:.:695,60,0
+chr1	931131	rs60722469	C	CCCCT	37940.21	PASS	AC=79;AF=0.608;AN=130;AS_BaseQRankSum=-0.200;AS_FS=19.073;AS_FilterStatus=PASS;AS_InbreedingCoeff=-0.0052;AS_MQ=60.00;AS_MQRankSum=0.000;AS_QD=29.01;AS_ReadPosRankSum=-0.500;AS_SOR=2.445;AS_VQSLOD=0.4905;AS_culprit=AS_FS;BaseQRankSum=-1.570e-01;DB;DP=2563;ExcessHet=2.0236;FS=19.073;InbreedingCoeff=-0.0052;MLEAC=78;MLEAF=0.600;MQ=59.99;MQRankSum=0.00;QD=29.01;ReadPosRankSum=-4.610e-01;SOR=2.423	GT:AD:DP:GQ:PGT:PID:PL	0/0:77,0:77:60	0/1:32,42:74:99:.:.:1059,0,906	0/1:13,49:62:99:0|1:931131_C_CCCCT:2016,0,224	0/1:15,32:47:99:0|1:931131_C_CCCCT:1367,0,378	0/1:14,8:22:99:.:.:293,0,698	1/1:0,18:18:52:.:.:706,52,0	0/0:34,0:34:60	0/0:36,0:36:60	0/1:7,15:22:99:.:.:698,0,285	1/1:0,21:21:62:.:.:890,62,0	0/1:18,11:29:99:.:.:358,0,893	0/1:8,6:14:99:.:.:201,0,424	0/1:6,9:15:99:.:.:319,0,282	0/1:18,13:31:99:.:.:501,0,836	1/1:0,23:23:68:.:.:970,68,0	0/1:17,11:28:99:.:.:398,0,699	1/1:0,19:19:57:.:.:843,57,0	0/1:7,13:20:99:.:.:492,0,245	0/0:34,0:34:60	0/1:8,8:16:99:.:.:306,0,370	1/1:1,12:13:10:.:.:510,10,0	0/1:6,10:16:99:.:.:471,0,249	0/1:12,8:20:99:.:.:315,0,591	0/1:7,9:16:99:.:.:345,0,358	1/1:0,32:32:98:.:.:1418,98,0	0/0:32,0:32:60	1/1:0,26:26:80:.:.:1171,80,0	1/1:0,30:30:95:.:.:1345,95,0	0/1:8,15:23:99:.:.:587,0,348	0/1:1,18:19:2:.:.:679,0,2	1/1:1,20:21:7:.:.:863,7,0	1/1:0,15:15:44:.:.:663,44,0	1/1:0,22:22:71:.:.:1046,71,0	0/0:47,0:47:60	0/1:9,7:16:99:.:.:249,0,398	0/1:13,12:25:99:.:.:426,0,650	0/1:18,11:29:99:.:.:443,0,687	1/1:1,18:19:11:.:.:720,11,0	0/1:17,15:32:99:.:.:496,0,796	0/1:8,12:20:99:.:.:447,0,307	1/1:1,15:16:22:.:.:697,22,0	0/1:10,7:17:99:.:.:252,0,505	1/1:0,25:25:80:.:.:1076,80,0	1/1:0,23:23:68:.:.:980,68,0	1/1:0,22:22:71:.:.:1024,71,0	1/1:0,12:12:38:.:.:536,38,0	0/1:18,12:30:99:.:.:468,0,672	0/0:43,0:43:60	0/0:32,0:32:60	1/1:1,29:30:47:.:.:1167,47,0	1/1:1,15:16:5:.:.:663,5,0	1/1:0,19:19:56:.:.:837,56,0	0/1:6,14:20:99:.:.:574,0,186	0/1:14,12:26:99:.:.:440,0,601	1/1:0,29:29:86:.:.:1247,86,0	0/1:12,5:17:99:.:.:201,0,646	1/1:1,21:22:23:.:.:788,23,0	0/1:12,11:23:99:.:.:436,0,487	0/0:37,0:37:60	0/0:35,0:35:60	1/1:0,13:13:38:.:.:552,38,0	0/1:8,15:23:99:.:.:559,0,290	0/1:11,9:22:99:.:.:281,0,582	1/1:0,23:23:74:.:.:1027,74,0	0/1:18,9:27:99:.:.:342,0,896
+chr1	931143	.	T	C	1125.29	VQSRTrancheSNP99.90to100.00+	AC=3;AF=0.023;AN=130;AS_BaseQRankSum=-2.700;AS_FS=342.391;AS_FilterStatus=VQSRTrancheSNP99.90to100.00+;AS_InbreedingCoeff=-0.0237;AS_MQ=59.70;AS_MQRankSum=0.000;AS_QD=5.18;AS_ReadPosRankSum=1.200;AS_SOR=8.051;AS_VQSLOD=-1081.5441;AS_culprit=AS_FS;BaseQRankSum=-2.622e+00;DP=2198;ExcessHet=0.1022;FS=342.391;InbreedingCoeff=-0.0237;MLEAC=3;MLEAF=0.023;MQ=59.92;MQRankSum=0.00;QD=5.19;ReadPosRankSum=1.30;SOR=8.051	GT:AD:DP:GQ:PGT:PID:PL	0/0:77,0:77:60	0/1:53,30:83:99:0|1:931143_T_C:742,0,2079	0/1:63,11:74:99:0|1:931143_T_C:116,0,2575	0/1:46,14:60:99:0|1:931143_T_C:308,0,1791	0/0:30,0:30:40	0/0:27,0:27:30	0/0:29,0:29:50	0/0:36,0:36:60	0/0:41,0:41:60	0/0:35,0:35:60	0/0:36,0:36:60	0/0:23,0:23:50	0/0:21,0:21:40	0/0:44,0:44:60	0/0:27,0:27:40	0/0:35,0:35:60	0/0:26,0:26:50	0/0:29,0:29:40	0/0:27,0:27:60	0/0:26,0:26:60	0/0:19,0:19:20	0/0:20,0:20:30	0/0:37,0:37:60	0/0:22,0:22:50	0/0:38,0:38:60	0/0:32,0:32:60	0/0:31,0:31:60	0/0:41,0:41:60	0/0:32,0:32:60	0/0:26,0:26:40	0/0:28,0:28:50	0/0:22,0:22:40	0/0:36,0:36:60	0/0:36,0:36:50	0/0:20,0:20:30	0/0:38,0:38:60	0/0:49,0:49:60	0/0:29,0:29:40	0/0:44,0:44:60	0/0:30,0:30:50	0/0:23,0:23:40	0/0:28,0:28:50	0/0:34,0:34:60	0/0:31,0:31:60	0/0:29,0:29:60	0/0:20,0:20:40	0/0:39,0:39:60	0/0:43,0:43:60	0/0:32,0:32:60	0/0:34,0:34:60	0/0:25,0:25:40	0/0:25,0:25:50	0/0:23,0:23:50	0/0:33,0:33:60	0/0:37,0:37:50	0/0:24,0:24:50	0/0:34,0:34:50	0/0:41,0:41:60	0/0:37,0:37:60	0/0:35,0:35:60	0/0:23,0:23:30	0/0:36,0:36:50	0/0:27,0:27:50	0/0:32,0:32:50	0/0:35,0:35:60
+chr1	935662	rs199537431	C	CA	1154.59	PASS	AC=1;AF=7.692e-03;AN=130;AS_BaseQRankSum=-0.900;AS_FS=0.000;AS_FilterStatus=PASS;AS_InbreedingCoeff=-0.0078;AS_MQ=60.00;AS_MQRankSum=0.000;AS_QD=18.33;AS_ReadPosRankSum=0.700;AS_SOR=0.933;AS_VQSLOD=1.7955;AS_culprit=AS_FS;BaseQRankSum=-8.390e-01;DB;DP=3105;ExcessHet=0.0000;FS=0.000;InbreedingCoeff=-0.0078;MLEAC=1;MLEAF=7.692e-03;MQ=60.00;MQRankSum=0.00;QD=18.33;ReadPosRankSum=0.895;SOR=1.000	GT:AD:DP:GQ:PL	0/0:71,0:71:60	0/0:29,0:29:60	0/0:29,0:29:60	0/0:22,0:22:50	0/0:32,0:32:60	0/0:36,0:36:60	0/0:39,0:39:60	0/0:37,0:37:60	0/0:41,0:41:60	0/0:38,0:38:60	0/0:38,0:38:60	0/0:50,0:50:60	0/0:34,0:34:60	0/0:38,0:38:60	0/0:41,0:41:60	0/0:51,0:51:60	0/0:39,0:39:60	0/0:40,0:40:60	0/0:189,0:189:60	0/0:38,0:38:60	0/0:37,0:37:60	0/0:38,0:38:60	0/0:43,0:43:60	0/0:45,0:45:60	0/0:45,0:45:60	0/0:45,0:45:60	0/0:36,0:36:60	0/0:45,0:45:60	0/0:40,0:40:60	0/0:36,0:36:60	0/0:53,0:53:60	0/0:50,0:50:60	0/0:40,0:40:60	0/0:47,0:47:60	0/1:28,35:65:99:1173,0,847	0/0:39,0:39:60	0/0:38,0:38:60	0/0:42,0:42:60	0/0:36,0:36:60	0/0:32,0:32:60	0/0:49,0:49:60	0/0:38,0:38:60	0/0:38,0:38:60	0/0:43,0:43:60	0/0:42,0:42:60	0/0:46,0:46:60	0/0:35,0:35:60	0/0:40,0:40:60	0/0:162,0:162:60	0/0:36,0:36:60	0/0:40,0:40:60	0/0:49,0:49:60	0/0:127,0:127:60	0/0:40,0:40:60	0/0:44,0:44:60	0/0:36,0:36:60	0/0:34,0:34:60	0/0:167,0:167:60	0/0:33,0:33:60	0/0:37,0:37:60	0/0:42,0:42:60	0/0:33,0:33:60	0/0:35,0:35:60	0/0:30,0:30:60	0/0:43,0:43:60
+chr1	935835	rs28419423	C	G	6303.83	PASS	AC=4;AF=0.031;AN=130;AS_BaseQRankSum=0.350;AS_FS=0.989;AS_FilterStatus=PASS;AS_InbreedingCoeff=-0.0317;AS_MQ=60.00;AS_MQRankSum=0.000;AS_QD=14.69;AS_ReadPosRankSum=0.650;AS_SOR=0.888;AS_VQSLOD=8.2068;AS_culprit=AS_ReadPosRankSum;BaseQRankSum=1.33;DB;DP=2885;ExcessHet=0.2060;FS=0.989;InbreedingCoeff=-0.0317;MLEAC=4;MLEAF=0.031;MQ=59.99;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=14.69;ReadPosRankSum=0.709;SOR=0.888	GT:AD:DP:GQ:PL	0/0:71,0:71:60	0/0:29,0:29:60	0/0:29,0:29:60	0/0:39,0:39:60	0/0:32,0:32:60	0/0:36,0:36:60	0/0:39,0:39:60	0/0:37,0:37:60	0/0:41,0:41:60	0/0:38,0:38:60	0/0:38,0:38:60	0/0:50,0:50:60	0/0:34,0:34:60	0/0:38,0:38:60	0/0:41,0:41:60	0/0:51,0:51:60	0/0:39,0:39:60	0/0:40,0:40:60	0/1:54,68:122:99:1802,0,1414	0/0:38,0:38:60	0/0:37,0:37:60	0/0:38,0:38:60	0/0:43,0:43:60	0/0:45,0:45:60	0/0:45,0:45:60	0/0:45,0:45:60	0/0:36,0:36:60	0/0:45,0:45:60	0/0:40,0:40:60	0/0:36,0:36:60	0/0:53,0:53:60	0/0:50,0:50:60	0/0:40,0:40:60	0/0:47,0:47:60	0/0:46,0:46:60	0/0:39,0:39:60	0/0:38,0:38:60	0/0:42,0:42:60	0/0:36,0:36:60	0/0:32,0:32:60	0/0:49,0:49:60	0/0:38,0:38:60	0/0:38,0:38:60	0/0:43,0:43:60	0/0:42,0:42:60	0/0:46,0:46:60	0/0:35,0:35:60	0/0:40,0:40:60	0/1:51,55:106:99:1512,0,1347	0/0:36,0:36:60	0/0:40,0:40:60	0/0:49,0:49:60	0/1:50,43:93:99:1189,0,1254	0/0:40,0:40:60	0/0:44,0:44:60	0/0:36,0:36:60	0/0:34,0:34:60	0/1:42,66:108:99:1850,0,1097	0/0:33,0:33:60	0/0:37,0:37:60	0/0:42,0:42:60	0/0:33,0:33:60	0/0:35,0:35:60	0/0:30,0:30:60	0/0:43,0:43:60
+chr1	939334	rs201596485	C	T	148.62	PASS	AC=1;AF=7.692e-03;AN=130;AS_BaseQRankSum=-1.400;AS_FS=0.000;AS_FilterStatus=PASS;AS_InbreedingCoeff=-0.0078;AS_MQ=60.00;AS_MQRankSum=0.000;AS_QD=6.77;AS_ReadPosRankSum=1.000;AS_SOR=0.446;AS_VQSLOD=6.6767;AS_culprit=AS_MQ;BaseQRankSum=-1.366e+00;DB;DP=2020;ExcessHet=0.0000;FS=0.000;InbreedingCoeff=-0.0078;MLEAC=1;MLEAF=7.692e-03;MQ=60.00;MQRankSum=0.00;QD=6.76;ReadPosRankSum=1.06;SOR=0.446	GT:AD:DP:GQ:PL	0/0:40,0:40:60	0/0:39,0:39:60	0/0:34,0:34:60	0/0:33,0:33:60	0/0:30,0:30:60	0/0:32,0:32:60	0/0:38,0:38:60	0/0:30,0:30:60	0/0:26,0:26:60	0/0:37,0:37:60	0/1:15,7:22:99:167,0,455	0/0:33,0:33:60	0/0:33,0:33:60	0/0:27,0:27:60	0/0:31,0:31:60	0/0:37,0:37:60	0/0:23,0:23:50	0/0:31,0:31:60	0/0:30,0:30:60	0/0:33,0:33:60	0/0:32,0:32:60	0/0:27,0:27:60	0/0:34,0:34:60	0/0:33,0:33:60	0/0:25,0:25:60	0/0:29,0:29:60	0/0:33,0:33:60	0/0:32,0:32:60	0/0:29,0:29:60	0/0:32,0:32:60	0/0:24,0:24:60	0/0:37,0:37:60	0/0:33,0:33:60	0/0:23,0:23:50	0/0:35,0:35:60	0/0:32,0:32:60	0/0:26,0:26:60	0/0:22,0:22:50	0/0:35,0:35:60	0/0:25,0:25:50	0/0:33,0:33:60	0/0:32,0:32:60	0/0:36,0:36:60	0/0:23,0:23:30	0/0:32,0:32:60	0/0:22,0:22:50	0/0:36,0:36:60	0/0:30,0:30:60	0/0:29,0:29:60	0/0:31,0:31:60	0/0:32,0:32:60	0/0:31,0:31:60	0/0:33,0:33:60	0/0:29,0:29:60	0/0:35,0:35:60	0/0:36,0:36:60	0/0:37,0:37:60	0/0:33,0:33:60	0/0:33,0:33:60	0/0:32,0:32:60	0/0:29,0:29:60	0/0:30,0:30:60	0/0:32,0:32:60	0/0:27,0:27:60	0/0:30,0:30:60
+chr1	939354	rs145967298	C	T	2198.83	PASS	AC=4;AF=0.031;AN=130;AS_BaseQRankSum=-0.400;AS_FS=1.470;AS_FilterStatus=PASS;AS_InbreedingCoeff=-0.0317;AS_MQ=60.00;AS_MQRankSum=0.000;AS_QD=14.96;AS_ReadPosRankSum=1.100;AS_SOR=0.864;AS_VQSLOD=7.0299;AS_culprit=AS_MQ;BaseQRankSum=-8.200e-02;DB;DP=2144;ExcessHet=0.2060;FS=1.470;InbreedingCoeff=-0.0317;MLEAC=4;MLEAF=0.031;MQ=60.00;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=14.96;ReadPosRankSum=1.62;SOR=0.864	GT:AD:DP:GQ:PL	0/0:40,0:40:60	0/0:39,0:39:60	0/0:34,0:34:60	0/0:33,0:33:60	0/0:30,0:30:60	0/0:32,0:32:60	0/0:38,0:38:60	0/0:30,0:30:60	0/0:26,0:26:60	0/0:37,0:37:60	0/0:26,0:26:60	0/0:33,0:33:60	0/0:33,0:33:60	0/0:27,0:27:60	0/0:31,0:31:60	0/0:37,0:37:60	0/0:33,0:33:60	0/0:31,0:31:60	0/0:30,0:30:60	0/0:33,0:33:60	0/0:32,0:32:60	0/0:27,0:27:60	0/0:34,0:34:60	0/0:33,0:33:60	0/0:36,0:36:60	0/0:29,0:29:60	0/0:33,0:33:60	0/1:21,22:43:99:551,0,581	0/0:29,0:29:60	0/0:32,0:32:60	0/0:21,0:21:50	0/0:37,0:37:60	0/0:33,0:33:60	0/0:39,0:39:60	0/0:35,0:35:60	0/1:13,17:30:99:491,0,337	0/0:37,0:37:60	0/0:32,0:32:60	0/0:35,0:35:60	0/0:27,0:27:40	0/0:33,0:33:60	0/0:32,0:32:60	0/0:36,0:36:60	0/0:33,0:33:60	0/0:40,0:40:60	0/0:35,0:35:60	0/0:36,0:36:60	0/0:31,0:31:60	0/0:29,0:29:60	0/0:31,0:31:60	0/0:32,0:32:60	0/0:35,0:35:60	0/0:33,0:33:60	0/0:29,0:29:60	0/0:35,0:35:60	0/0:36,0:36:60	0/1:18,22:40:99:584,0,460	0/0:33,0:33:60	0/0:33,0:33:60	0/0:32,0:32:60	0/1:12,22:34:99:622,0,295	0/0:30,0:30:60	0/0:32,0:32:60	0/0:34,0:34:60	0/0:30,0:30:60
+chr1	939484	rs141512630	CT	C	176.59	VQSRTrancheINDEL95.00to96.00	AC=1;AF=7.692e-03;AN=130;AS_BaseQRankSum=0.500;AS_FS=3.402;AS_FilterStatus=VQSRTrancheINDEL95.00to96.00;AS_InbreedingCoeff=-0.0078;AS_MQ=58.47;AS_MQRankSum=-1.700;AS_QD=4.02;AS_ReadPosRankSum=-1.500;AS_SOR=0.268;AS_VQSLOD=-0.5692;AS_culprit=AS_MQRankSum;BaseQRankSum=0.501;DB;DP=2255;ExcessHet=0.0000;FS=3.402;InbreedingCoeff=-0.0078;MLEAC=1;MLEAF=7.692e-03;MQ=59.62;MQRankSum=-1.680e+00;QD=4.01;ReadPosRankSum=-1.425e+00;SOR=0.268	GT:AD:DP:GQ:PL	0/0:40,0:40:60	0/0:39,0:39:60	0/0:34,0:34:60	0/0:33,0:33:60	0/0:93,0:93:60	0/0:32,0:32:60	0/0:38,0:38:60	0/0:30,0:30:60	0/0:37,0:37:60	0/0:37,0:37:60	0/0:26,0:26:60	0/0:33,0:33:60	0/0:33,0:33:60	0/0:27,0:27:60	0/0:31,0:31:60	0/0:37,0:37:60	0/0:33,0:33:60	0/0:31,0:31:60	0/0:30,0:30:60	0/0:32,0:32:50	0/0:42,0:42:60	0/0:35,0:35:60	0/0:34,0:34:60	0/0:33,0:33:60	0/0:38,0:38:60	0/0:29,0:29:60	0/0:46,0:46:60	0/0:42,0:42:60	0/0:29,0:29:60	0/0:26,0:26:50	0/0:31,0:31:60	0/0:42,0:42:60	0/0:33,0:33:60	0/0:39,0:39:60	0/0:33,0:33:60	0/0:36,0:36:60	0/0:37,0:37:60	0/0:32,0:32:60	0/0:35,0:35:60	0/0:33,0:33:60	0/0:33,0:33:60	0/0:32,0:32:60	0/0:25,0:25:60	0/0:33,0:33:60	0/0:40,0:40:60	0/0:21,0:21:60	0/0:29,0:29:60	0/0:31,0:31:60	0/0:29,0:29:60	0/1:33,11:44:99:195,0,1063	0/0:32,0:32:60	0/0:35,0:35:60	0/0:33,0:33:60	0/0:29,0:29:60	0/0:41,0:41:60	0/0:36,0:36:60	0/0:39,0:39:60	0/0:33,0:33:60	0/0:33,0:33:60	0/0:32,0:32:60	0/0:38,0:38:60	0/0:30,0:30:60	0/0:32,0:32:60	0/0:34,0:34:60	0/0:30,0:30:60
+chr1	943045	.	C	T	414.32	PASS	AC=2;AF=0.015;AN=130;AS_BaseQRankSum=-0.150;AS_FS=1.189;AS_FilterStatus=PASS;AS_InbreedingCoeff=-0.0165;AS_MQ=60.00;AS_MQRankSum=0.000;AS_QD=9.20;AS_ReadPosRankSum=0.900;AS_SOR=0.410;AS_VQSLOD=5.9634;AS_culprit=AS_MQ;BaseQRankSum=0.717;DP=1439;ExcessHet=0.0338;FS=1.189;InbreedingCoeff=-0.0166;MLEAC=2;MLEAF=0.015;MQ=60.00;MQRankSum=0.00;QD=9.21;ReadPosRankSum=1.37;SOR=0.410	GT:AD:DP:GQ:PL	0/0:18,0:18:50	0/0:12,0:12:30	0/0:13,0:13:30	0/0:8,0:8:20	0/0:28,0:28:60	0/0:23,0:23:50	0/0:29,0:29:60	0/0:26,0:26:60	0/0:13,0:13:30	0/0:24,0:24:60	0/0:21,0:21:50	0/0:25,0:25:60	0/0:13,0:13:30	0/0:27,0:27:60	0/0:19,0:19:50	0/0:29,0:29:60	0/1:11,9:20:99:233,0,282	0/0:32,0:32:60	0/0:24,0:24:40	0/0:26,0:26:60	0/0:17,0:17:50	0/0:18,0:18:50	0/0:28,0:28:60	0/0:31,0:31:60	0/0:22,0:22:60	0/0:24,0:24:60	0/0:15,0:15:30	0/0:26,0:26:60	0/0:19,0:19:50	0/0:13,0:13:30	0/0:13,0:13:30	0/0:18,0:18:40	0/0:24,0:24:60	0/0:25,0:25:60	0/0:12,0:12:30	0/0:28,0:28:60	0/0:25,0:25:40	0/0:16,0:16:40	0/0:27,0:27:60	0/0:15,0:15:10	0/0:20,0:20:50	0/0:22,0:22:60	0/0:21,0:21:50	0/0:27,0:27:60	0/0:24,0:24:60	0/0:28,0:28:60	0/0:26,0:26:60	0/0:23,0:23:50	0/0:31,0:31:60	0/0:24,0:24:60	0/0:12,0:12:30	0/0:30,0:30:60	0/0:18,0:18:40	0/0:31,0:31:60	0/0:24,0:24:60	0/0:21,0:21:60	0/0:17,0:17:40	0/0:20,0:20:40	0/0:19,0:19:50	0/0:21,0:21:50	0/0:13,0:13:30	0/0:36,0:36:60	0/0:30,0:30:60	0/1:15,10:25:99:212,0,384	0/0:29,0:29:60
+chr1	943136	rs201043644	GA	G	551.35	PASS	AC=2;AF=0.015;AN=130;AS_BaseQRankSum=.;AS_FS=0.000;AS_FilterStatus=PASS;AS_InbreedingCoeff=0.8072;AS_MQ=60.00;AS_MQRankSum=.;AS_QD=30.61;AS_ReadPosRankSum=.;AS_SOR=0.914;AS_VQSLOD=3.9455;AS_culprit=AS_FS;DB;DP=957;ExcessHet=0.0000;FS=0.000;InbreedingCoeff=0.7976;MLEAC=2;MLEAF=0.015;MQ=60.00;POSITIVE_TRAIN_SITE;QD=30.63;SOR=0.914	GT:AD:DP:GQ:PL	0/0:24,0:24:50	0/0:27,0:27:60	0/0:18,0:18:50	0/0:28,0:28:60	1/1:0,18:18:54:588,54,0	0/0:15,0:15:30	0/0:15,0:15:30	0/0:22,0:22:50	0/0:12,0:12:20	0/0:15,0:15:30	0/0:13,0:13:30	0/0:11,0:11:20	0/0:14,0:14:30	0/0:13,0:13:30	0/0:12,0:12:20	0/0:19,0:19:40	0/0:9,0:9:20	0/0:15,0:15:30	0/0:18,0:18:40	0/0:12,0:12:30	0/0:11,0:11:20	0/0:12,0:12:30	0/0:18,0:18:40	0/0:18,0:18:30	0/0:17,0:17:40	0/0:11,0:11:20	0/0:18,0:18:40	0/0:17,0:17:40	0/0:14,0:14:30	0/0:8,0:8:20	0/0:10,0:10:20	0/0:18,0:18:40	0/0:10,0:10:20	0/0:13,0:13:30	0/0:14,0:14:30	0/0:22,0:22:50	0/0:13,0:13:30	0/0:13,0:13:30	0/0:10,0:10:20	0/0:8,0:8:10	0/0:17,0:17:40	0/0:12,0:12:20	0/0:15,0:15:30	0/0:13,0:13:30	0/0:18,0:18:40	0/0:14,0:14:30	0/0:17,0:17:10	0/0:9,0:9:20	0/0:13,0:13:30	0/0:17,0:17:40	0/0:11,0:11:20	0/0:20,0:20:40	0/0:12,0:12:20	0/0:14,0:14:30	0/0:14,0:14:40	0/0:10,0:10:20	0/0:11,0:11:20	0/0:13,0:13:30	0/0:15,0:15:30	0/0:13,0:13:30	0/0:14,0:14:30	0/0:12,0:12:20	0/0:19,0:19:40	0/0:8,0:8:10	0/0:21,0:21:50
+chr1	943365	rs72902602	A	C	661.62	PASS	AC=1;AF=7.692e-03;AN=130;AS_BaseQRankSum=0.200;AS_FS=0.000;AS_FilterStatus=PASS;AS_InbreedingCoeff=-0.0078;AS_MQ=60.00;AS_MQRankSum=0.000;AS_QD=10.68;AS_ReadPosRankSum=0.400;AS_SOR=0.811;AS_VQSLOD=7.2847;AS_culprit=AS_MQ;BaseQRankSum=0.245;DB;DP=2151;ExcessHet=0.0000;FS=0.000;InbreedingCoeff=-0.0078;MLEAC=1;MLEAF=7.692e-03;MQ=60.00;MQRankSum=0.00;QD=10.67;ReadPosRankSum=0.467;SOR=0.811	GT:AD:DP:GQ:PL	0/0:30,0:30:60	0/0:16,0:16:30	0/0:25,0:25:50	0/0:22,0:22:50	0/1:28,34:62:99:680,0,527	0/0:36,0:36:60	0/0:33,0:33:60	0/0:29,0:29:60	0/0:32,0:32:60	0/0:34,0:34:60	0/0:34,0:34:60	0/0:31,0:31:60	0/0:34,0:34:60	0/0:30,0:30:60	0/0:31,0:31:60	0/0:37,0:37:60	0/0:32,0:32:60	0/0:34,0:34:60	0/0:37,0:37:60	0/0:34,0:34:60	0/0:36,0:36:60	0/0:34,0:34:60	0/0:32,0:32:60	0/0:31,0:31:60	0/0:34,0:34:60	0/0:33,0:33:60	0/0:38,0:38:60	0/0:31,0:31:60	0/0:31,0:31:60	0/0:34,0:34:60	0/0:30,0:30:60	0/0:37,0:37:60	0/0:31,0:31:60	0/0:32,0:32:60	0/0:33,0:33:60	0/0:35,0:35:60	0/0:32,0:32:60	0/0:31,0:31:60	0/0:36,0:36:60	0/0:34,0:34:60	0/0:31,0:31:60	0/0:33,0:33:60	0/0:35,0:35:60	0/0:34,0:34:60	0/0:32,0:32:60	0/0:35,0:35:60	0/0:34,0:34:60	0/0:33,0:33:60	0/0:36,0:36:60	0/0:34,0:34:60	0/0:34,0:34:60	0/0:31,0:31:60	0/0:33,0:33:60	0/0:35,0:35:60	0/0:31,0:31:60	0/0:36,0:36:60	0/0:32,0:32:60	0/0:34,0:34:60	0/0:34,0:34:60	0/0:30,0:30:60	0/0:34,0:34:60	0/0:33,0:33:60	0/0:33,0:33:60	0/0:32,0:32:60	0/0:33,0:33:60
+chr1	943429	rs191952374	C	T	1116.29	PASS	AC=2;AF=0.015;AN=130;AS_BaseQRankSum=1.700;AS_FS=7.671;AS_FilterStatus=PASS;AS_InbreedingCoeff=-0.0156;AS_MQ=60.00;AS_MQRankSum=0.000;AS_QD=15.08;AS_ReadPosRankSum=0.600;AS_SOR=2.124;AS_VQSLOD=5.7096;AS_culprit=AS_MQ;BaseQRankSum=2.01;DB;DP=2074;ExcessHet=0.0338;FS=7.671;InbreedingCoeff=-0.0156;MLEAC=2;MLEAF=0.015;MQ=60.00;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=15.08;ReadPosRankSum=1.48;SOR=2.124	GT:AD:DP:GQ:PL	0/0:18,0:18:50	0/0:16,0:16:40	0/0:16,0:16:40	0/0:15,0:15:40	0/0:22,0:22:50	0/0:36,0:36:60	0/0:33,0:33:60	0/0:29,0:29:60	0/0:32,0:32:60	0/0:34,0:34:60	0/0:34,0:34:60	0/0:31,0:31:60	0/0:34,0:34:60	0/0:30,0:30:60	0/0:31,0:31:60	0/0:37,0:37:60	0/0:32,0:32:60	0/0:34,0:34:60	0/0:37,0:37:60	0/0:34,0:34:60	0/0:36,0:36:60	0/0:34,0:34:60	0/0:32,0:32:60	0/0:31,0:31:60	0/0:34,0:34:60	0/0:33,0:33:60	0/0:34,0:34:60	0/0:31,0:31:60	0/0:31,0:31:60	0/1:18,16:34:99:454,0,483	0/0:30,0:30:60	0/0:37,0:37:60	0/0:31,0:31:60	0/0:32,0:32:60	0/0:33,0:33:60	0/0:35,0:35:60	0/0:32,0:32:60	0/0:31,0:31:60	0/0:36,0:36:60	0/0:34,0:34:60	0/0:22,0:22:40	0/0:33,0:33:60	0/0:35,0:35:60	0/0:34,0:34:60	0/0:32,0:32:60	0/1:16,24:40:99:693,0,395	0/0:34,0:34:60	0/0:33,0:33:60	0/0:36,0:36:60	0/0:34,0:34:60	0/0:34,0:34:60	0/0:31,0:31:60	0/0:33,0:33:60	0/0:35,0:35:60	0/0:31,0:31:60	0/0:36,0:36:60	0/0:32,0:32:60	0/0:34,0:34:60	0/0:34,0:34:60	0/0:30,0:30:60	0/0:34,0:34:60	0/0:33,0:33:60	0/0:33,0:33:60	0/0:32,0:32:60	0/0:33,0:33:60
+chr1	943937	rs7523549	C	T	984.62	PASS	AC=1;AF=7.692e-03;AN=130;AS_BaseQRankSum=0.800;AS_FS=6.350;AS_FilterStatus=PASS;AS_InbreedingCoeff=-0.0078;AS_MQ=60.00;AS_MQRankSum=0.000;AS_QD=14.28;AS_ReadPosRankSum=-1.800;AS_SOR=1.118;AS_VQSLOD=5.5451;AS_culprit=AS_ReadPosRankSum;BaseQRankSum=0.837;DB;DP=2269;ExcessHet=0.0000;FS=6.350;InbreedingCoeff=-0.0078;MLEAC=1;MLEAF=7.692e-03;MQ=60.00;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=14.27;ReadPosRankSum=-1.755e+00;SOR=1.118	GT:AD:DP:GQ:PL	0/0:30,0:30:60	0/0:37,0:37:60	0/0:31,0:31:60	0/0:31,0:31:60	0/0:29,0:29:60	0/0:32,0:32:60	0/0:35,0:35:60	0/0:43,0:43:60	0/0:31,0:31:60	0/0:36,0:36:60	0/0:34,0:34:60	0/0:32,0:32:60	0/0:36,0:36:60	0/0:37,0:37:60	0/0:39,0:39:60	0/0:40,0:40:60	0/0:32,0:32:60	0/0:33,0:33:60	0/0:33,0:33:60	0/0:34,0:34:60	0/0:33,0:33:60	0/0:37,0:37:60	0/0:41,0:41:60	0/0:35,0:35:60	0/0:36,0:36:60	0/0:33,0:33:60	0/0:33,0:33:60	0/0:34,0:34:60	0/0:31,0:31:60	0/0:36,0:36:60	0/0:34,0:34:60	0/0:34,0:34:60	0/0:31,0:31:60	0/0:34,0:34:60	0/0:40,0:40:60	0/0:35,0:35:60	0/0:36,0:36:60	0/0:37,0:37:60	0/0:33,0:33:60	0/0:32,0:32:60	0/0:32,0:32:60	0/0:38,0:38:60	0/0:37,0:37:60	0/0:31,0:31:60	0/0:38,0:38:60	0/0:41,0:41:60	0/0:37,0:37:60	0/0:35,0:35:60	0/0:36,0:36:60	0/1:33,36:69:99:1003,0,879	0/0:34,0:34:60	0/0:33,0:33:60	0/0:33,0:33:60	0/0:32,0:32:60	0/0:31,0:31:60	0/0:33,0:33:60	0/0:32,0:32:60	0/0:31,0:31:60	0/0:31,0:31:60	0/0:32,0:32:60	0/0:30,0:30:60	0/0:32,0:32:60	0/0:37,0:37:60	0/0:36,0:36:60	0/0:38,0:38:60
+chr1	944795	.	C	T	296.62	PASS	AC=1;AF=7.692e-03;AN=130;AS_BaseQRankSum=-1.800;AS_FS=0.000;AS_FilterStatus=PASS;AS_InbreedingCoeff=-0.0078;AS_MQ=60.00;AS_MQRankSum=1.500;AS_QD=12.38;AS_ReadPosRankSum=0.300;AS_SOR=0.317;AS_VQSLOD=0.7709;AS_culprit=AS_MQRankSum;BaseQRankSum=-1.762e+00;DP=1918;ExcessHet=0.0000;FS=0.000;InbreedingCoeff=-0.0078;MLEAC=1;MLEAF=7.692e-03;MQ=58.66;MQRankSum=1.51;QD=12.36;ReadPosRankSum=0.318;SOR=0.317	GT:AD:DP:GQ:PL	0/0:31,0:31:60	0/0:34,0:34:60	0/0:34,0:34:60	0/0:28,0:28:60	0/0:13,0:13:30	0/0:32,0:32:60	0/0:32,0:32:60	0/0:36,0:36:60	0/0:29,0:29:60	0/0:34,0:34:60	0/0:31,0:31:60	0/0:32,0:32:60	0/0:31,0:31:60	0/0:35,0:35:60	0/0:35,0:35:60	0/0:33,0:33:60	0/0:28,0:28:60	0/0:32,0:32:60	0/1:12,12:24:99:315,0,342	0/0:26,0:26:50	0/0:24,0:24:50	0/0:16,0:16:30	0/0:34,0:34:60	0/0:30,0:30:60	0/0:34,0:34:60	0/0:27,0:27:60	0/0:28,0:28:60	0/0:28,0:28:60	0/0:30,0:30:60	0/0:19,0:19:30	0/0:33,0:33:60	0/0:31,0:31:60	0/0:26,0:26:60	0/0:20,0:20:40	0/0:38,0:38:60	0/0:36,0:36:60	0/0:30,0:30:60	0/0:28,0:28:60	0/0:23,0:23:50	0/0:34,0:34:60	0/0:35,0:35:60	0/0:31,0:31:60	0/0:38,0:38:60	0/0:35,0:35:60	0/0:27,0:27:60	0/0:31,0:31:60	0/0:26,0:26:60	0/0:23,0:23:50	0/0:24,0:24:50	0/0:25,0:25:60	0/0:36,0:36:60	0/0:35,0:35:60	0/0:34,0:34:60	0/0:35,0:35:60	0/0:26,0:26:60	0/0:32,0:32:60	0/0:34,0:34:60	0/0:27,0:27:60	0/0:28,0:28:60	0/0:34,0:34:60	0/0:27,0:27:60	0/0:19,0:19:40	0/0:20,0:20:50	0/0:26,0:26:60	0/0:30,0:30:60
+chr1	945010	rs3748593	C	A	531.62	PASS	AC=1;AF=7.692e-03;AN=130;AS_BaseQRankSum=1.800;AS_FS=0.000;AS_FilterStatus=PASS;AS_InbreedingCoeff=-0.0078;AS_MQ=60.00;AS_MQRankSum=0.000;AS_QD=10.64;AS_ReadPosRankSum=-0.700;AS_SOR=0.632;AS_VQSLOD=8.4110;AS_culprit=AS_MQ;BaseQRankSum=1.83;DB;DP=2238;ExcessHet=0.0000;FS=0.000;InbreedingCoeff=-0.0078;MLEAC=1;MLEAF=7.692e-03;MQ=60.00;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=10.63;ReadPosRankSum=-6.690e-01;SOR=0.632	GT:AD:DP:GQ:PL	0/0:36,0:36:60	0/0:30,0:30:60	0/0:34,0:34:60	0/0:37,0:37:60	0/0:27,0:27:60	0/0:36,0:36:60	0/0:38,0:38:60	0/0:35,0:35:60	0/0:35,0:35:60	0/0:30,0:30:60	0/0:34,0:34:60	0/0:32,0:32:60	0/0:30,0:30:60	0/0:39,0:39:60	0/0:32,0:32:60	0/0:31,0:31:60	0/0:32,0:32:60	0/0:29,0:29:60	0/0:37,0:37:60	0/0:31,0:31:60	0/0:33,0:33:60	0/0:33,0:33:60	0/0:35,0:35:60	0/0:32,0:32:60	0/0:33,0:33:60	0/0:36,0:36:60	0/0:35,0:35:60	0/0:34,0:34:60	0/0:34,0:34:60	0/0:33,0:33:60	0/0:37,0:37:60	0/0:32,0:32:60	0/0:34,0:34:60	0/0:29,0:29:60	0/0:34,0:34:60	0/0:33,0:33:60	0/0:31,0:31:60	0/0:40,0:40:60	0/0:36,0:36:60	0/0:35,0:35:60	0/0:33,0:33:60	0/0:33,0:33:60	0/0:31,0:31:60	0/0:34,0:34:60	0/0:34,0:34:60	0/0:34,0:34:60	0/0:66,0:66:60	0/0:37,0:37:60	0/0:31,0:31:60	0/1:29,21:50:99:550,0,746	0/0:32,0:32:60	0/0:35,0:35:60	0/0:32,0:32:60	0/0:35,0:35:60	0/0:33,0:33:60	0/0:36,0:36:60	0/0:40,0:40:60	0/0:34,0:34:60	0/0:31,0:31:60	0/0:41,0:41:60	0/0:35,0:35:60	0/0:33,0:33:60	0/0:36,0:36:60	0/0:31,0:31:60	0/0:27,0:27:60
+chr1	945086	rs138652036	T	C	479.62	PASS	AC=1;AF=7.692e-03;AN=130;AS_BaseQRankSum=-0.400;AS_FS=5.931;AS_FilterStatus=PASS;AS_InbreedingCoeff=-0.0078;AS_MQ=60.00;AS_MQRankSum=0.000;AS_QD=9.60;AS_ReadPosRankSum=-2.100;AS_SOR=0.162;AS_VQSLOD=4.0849;AS_culprit=AS_ReadPosRankSum;BaseQRankSum=-3.330e-01;DB;DP=2188;ExcessHet=0.0000;FS=5.931;InbreedingCoeff=-0.0078;MLEAC=1;MLEAF=7.692e-03;MQ=60.00;MQRankSum=0.00;QD=9.59;ReadPosRankSum=-2.087e+00;SOR=0.162	GT:AD:DP:GQ:PL	0/0:36,0:36:60	0/0:30,0:30:60	0/0:34,0:34:60	0/0:37,0:37:60	0/0:27,0:27:60	0/0:36,0:36:60	0/0:38,0:38:60	0/0:35,0:35:60	0/0:35,0:35:60	0/0:30,0:30:60	0/0:34,0:34:60	0/0:32,0:32:60	0/0:30,0:30:60	0/0:39,0:39:60	0/0:32,0:32:60	0/0:31,0:31:60	0/0:32,0:32:60	0/0:29,0:29:60	0/0:24,0:24:50	0/0:31,0:31:60	0/0:33,0:33:60	0/0:33,0:33:60	0/0:35,0:35:60	0/0:32,0:32:60	0/0:33,0:33:60	0/0:36,0:36:60	0/0:35,0:35:60	0/0:34,0:34:60	0/0:34,0:34:60	0/0:33,0:33:60	0/0:37,0:37:60	0/0:32,0:32:60	0/0:34,0:34:60	0/0:29,0:29:60	0/0:34,0:34:60	0/0:33,0:33:60	0/0:31,0:31:60	0/0:40,0:40:60	0/0:36,0:36:60	0/0:35,0:35:60	0/0:33,0:33:60	0/0:33,0:33:60	0/0:31,0:31:60	0/0:34,0:34:60	0/0:34,0:34:60	0/0:34,0:34:60	0/1:29,21:50:99:498,0,759	0/0:37,0:37:60	0/0:31,0:31:60	0/0:39,0:39:60	0/0:32,0:32:60	0/0:35,0:35:60	0/0:32,0:32:60	0/0:35,0:35:60	0/0:33,0:33:60	0/0:36,0:36:60	0/0:30,0:30:60	0/0:34,0:34:60	0/0:31,0:31:60	0/0:41,0:41:60	0/0:35,0:35:60	0/0:33,0:33:60	0/0:36,0:36:60	0/0:31,0:31:60	0/0:27,0:27:60
+chr1	945573	rs138129954	G	A	2776.29	PASS	AC=2;AF=0.015;AN=130;AS_BaseQRankSum=0.150;AS_FS=0.000;AS_FilterStatus=PASS;AS_InbreedingCoeff=-0.0156;AS_MQ=54.63;AS_MQRankSum=-0.550;AS_QD=11.24;AS_ReadPosRankSum=-0.300;AS_SOR=0.730;AS_VQSLOD=2.7778;AS_culprit=AS_MQRankSum;BaseQRankSum=1.39;DB;DP=2431;ExcessHet=0.0338;FS=0.000;InbreedingCoeff=-0.0156;MLEAC=2;MLEAF=0.015;MQ=54.82;MQRankSum=0.333;QD=11.24;ReadPosRankSum=0.030;SOR=0.730	GT:AD:DP:GQ:PL	0/0:36,0:36:60	0/0:33,0:33:60	0/0:39,0:39:60	0/0:30,0:30:60	0/0:29,0:29:60	0/0:33,0:33:60	0/0:30,0:30:60	0/0:35,0:35:60	0/0:37,0:37:60	0/0:28,0:28:60	0/0:32,0:32:60	0/1:66,52:118:99:1263,0,1714	0/0:30,0:30:60	0/0:36,0:36:60	0/0:64,0:64:60	0/0:34,0:34:60	0/0:36,0:36:60	0/0:32,0:32:60	0/0:35,0:35:60	0/0:32,0:32:60	0/0:32,0:32:60	0/0:28,0:28:60	0/0:30,0:30:60	0/0:32,0:32:60	0/0:34,0:34:60	0/0:32,0:32:60	0/0:28,0:28:60	0/0:34,0:34:60	0/0:31,0:31:60	0/0:31,0:31:60	0/0:32,0:32:60	0/0:31,0:31:60	0/0:31,0:31:60	0/0:34,0:34:60	0/0:32,0:32:60	0/0:38,0:38:60	0/0:117,0:117:60	0/0:26,0:26:60	0/0:33,0:33:60	0/0:32,0:32:60	0/1:71,58:129:99:1544,0,1802	0/0:34,0:34:60	0/0:37,0:37:60	0/0:33,0:33:60	0/0:34,0:34:60	0/0:33,0:33:60	0/0:66,0:66:60	0/0:34,0:34:60	0/0:31,0:31:60	0/0:33,0:33:60	0/0:28,0:28:60	0/0:29,0:29:60	0/0:34,0:34:60	0/0:30,0:30:60	0/0:34,0:34:60	0/0:32,0:32:60	0/0:34,0:34:60	0/0:35,0:35:60	0/0:31,0:31:60	0/0:27,0:27:60	0/0:33,0:33:60	0/0:30,0:30:60	0/0:34,0:34:60	0/0:28,0:28:60	0/0:31,0:31:60
+chr1	945670	rs374558436	C	T	1359.63	PASS	AC=1;AF=7.692e-03;AN=130;AS_BaseQRankSum=-3.400;AS_FS=0.911;AS_FilterStatus=PASS;AS_InbreedingCoeff=-0.0078;AS_MQ=60.00;AS_MQRankSum=0.000;AS_QD=14.47;AS_ReadPosRankSum=0.300;AS_SOR=0.581;AS_VQSLOD=7.7760;AS_culprit=AS_MQ;BaseQRankSum=-3.393e+00;DB;DP=2288;ExcessHet=0.0000;FS=0.911;InbreedingCoeff=-0.0078;MLEAC=1;MLEAF=7.692e-03;MQ=60.00;MQRankSum=0.00;QD=14.46;ReadPosRankSum=0.320;SOR=0.581	GT:AD:DP:GQ:PL	0/0:36,0:36:60	0/0:33,0:33:60	0/0:39,0:39:60	0/0:30,0:30:60	0/0:29,0:29:60	0/0:33,0:33:60	0/0:30,0:30:60	0/0:35,0:35:60	0/0:37,0:37:60	0/0:28,0:28:60	0/0:32,0:32:60	0/0:38,0:38:60	0/0:30,0:30:60	0/0:36,0:36:60	0/0:64,0:64:60	0/0:34,0:34:60	0/0:36,0:36:60	0/0:32,0:32:60	0/0:35,0:35:60	0/0:32,0:32:60	0/0:32,0:32:60	0/0:28,0:28:60	0/0:30,0:30:60	0/0:32,0:32:60	0/0:34,0:34:60	0/0:32,0:32:60	0/0:28,0:28:60	0/0:34,0:34:60	0/0:31,0:31:60	0/0:31,0:31:60	0/0:32,0:32:60	0/0:31,0:31:60	0/0:31,0:31:60	0/0:34,0:34:60	0/0:32,0:32:60	0/0:38,0:38:60	0/0:117,0:117:60	0/0:26,0:26:60	0/0:33,0:33:60	0/0:32,0:32:60	0/0:38,0:38:60	0/0:34,0:34:60	0/0:37,0:37:60	0/0:33,0:33:60	0/0:34,0:34:60	0/0:33,0:33:60	0/1:41,53:94:99:1378,0,1117	0/0:34,0:34:60	0/0:31,0:31:60	0/0:33,0:33:60	0/0:28,0:28:60	0/0:29,0:29:60	0/0:34,0:34:60	0/0:30,0:30:60	0/0:34,0:34:60	0/0:32,0:32:60	0/0:34,0:34:60	0/0:35,0:35:60	0/0:31,0:31:60	0/0:27,0:27:60	0/0:33,0:33:60	0/0:30,0:30:60	0/0:34,0:34:60	0/0:28,0:28:60	0/0:31,0:31:60
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/expected.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/expected.vcf.idx
new file mode 100644
index 00000000000..545d172029e
Binary files /dev/null and b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/expected.vcf.idx differ
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/expected/empty_file.txt b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/expected/empty_file.txt
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/expected/expected_warning_as_vqslod.txt b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/expected/expected_warning_as_vqslod.txt
new file mode 100644
index 00000000000..ba4d380a12a
--- /dev/null
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/expected/expected_warning_as_vqslod.txt
@@ -0,0 +1 @@
+At position chr1:186475 Variant contexts have different attribute values for AS_VQSLOD: actual has -4.8149 and expected has -3.2178
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/expected/expected_warning_filter.txt b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/expected/expected_warning_filter.txt
new file mode 100644
index 00000000000..71290b47f92
--- /dev/null
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/expected/expected_warning_filter.txt
@@ -0,0 +1 @@
+At position chr1:187471 Variant contexts have different attribute values for AS_FilterStatus: actual has VQSRTrancheSNP99.00to99.90+ and expected has VQSRTrancheSNP99.90to100.00+
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/expected/haploid_warning.txt b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/expected/haploid_warning.txt
new file mode 100644
index 00000000000..e49dc746145
--- /dev/null
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/expected/haploid_warning.txt
@@ -0,0 +1 @@
+At position chrX:66780645 Genotypes have different alleles: actual has [CT] expected has [CT, CT]
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/expected/haploid_warning2.txt b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/expected/haploid_warning2.txt
new file mode 100644
index 00000000000..4c8f4ccb983
--- /dev/null
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/expected/haploid_warning2.txt
@@ -0,0 +1 @@
+At position chrX:66780645 Genotypes have different alleles: actual has [CT, CT] expected has [CT]
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/expected/qual_diff_warning.txt b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/expected/qual_diff_warning.txt
new file mode 100644
index 00000000000..edf6e9481ee
--- /dev/null
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/expected/qual_diff_warning.txt
@@ -0,0 +1 @@
+At position chr1:945670 qual scores differ by 0.010000000000218279, which is more than 0.001
\ No newline at end of file
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/expected/ref_block_warning.txt b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/expected/ref_block_warning.txt
new file mode 100644
index 00000000000..08bd23b1aa1
--- /dev/null
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/expected/ref_block_warning.txt
@@ -0,0 +1,2 @@
+At position chr1:54682 Variant contexts have different attribute values for END: actual has 207666 and expected has 207668
+Unmatched variant in actual at position chr1:257667
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/expected/tree_score_warning.txt b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/expected/tree_score_warning.txt
new file mode 100644
index 00000000000..3275b4a0748
--- /dev/null
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/expected/tree_score_warning.txt
@@ -0,0 +1 @@
+At position chr1:792417 Variant contexts have different attribute values for TREE_SCORE: actual has 0.311083 and expected has 0.372848
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/haploid.rb.g.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/haploid.rb.g.vcf
new file mode 100644
index 00000000000..3b618fa7da1
--- /dev/null
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/haploid.rb.g.vcf
@@ -0,0 +1,64 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths (counting only informative reads out of the total reads) for the ref and alt alleles in the order listed">
+##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele fractions for alt alleles in the order listed">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
+##FORMAT=<ID=F1R2,Number=R,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting each allele">
+##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele">
+##FORMAT=<ID=GP,Number=G,Type=Float,Description="Phred-scaled posterior probabilities for genotypes as defined in the VCF specification">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=ICNT,Number=2,Type=Integer,Description="Counts of INDEL informative reads based on the reference confidence model">
+##FORMAT=<ID=MB,Number=4,Type=Integer,Description="Per-sample component statistics to detect mate bias">
+##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##FORMAT=<ID=PRI,Number=G,Type=Float,Description="Phred-scaled prior probabilities for genotypes">
+##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
+##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias">
+##FORMAT=<ID=SPL,Number=.,Type=Integer,Description="Normalized, Phred-scaled likelihoods for SNPs based on the reference confidence model">
+##FORMAT=<ID=SQ,Number=1,Type=Float,Description="Somatic quality">
+##GVCFBlock0-20=minGQ=0(inclusive),maxGQ=20(exclusive)
+##GVCFBlock20-30=minGQ=20(inclusive),maxGQ=30(exclusive)
+##GVCFBlock30-40=minGQ=30(inclusive),maxGQ=40(exclusive)
+##GVCFBlock40-100=minGQ=40(inclusive),maxGQ=100(exclusive)
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=AS_BaseQRankSum,Number=A,Type=Float,Description="allele specific Z-score from Wilcoxon rank sum test of each Alt Vs. Ref base qualities">
+##INFO=<ID=AS_FS,Number=A,Type=Float,Description="allele specific phred-scaled p-value using Fisher's exact test to detect strand bias of each alt allele">
+##INFO=<ID=AS_InbreedingCoeff,Number=A,Type=Float,Description="Allele-specific inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
+##INFO=<ID=AS_MQ,Number=A,Type=Float,Description="Allele-specific RMS Mapping Quality">
+##INFO=<ID=AS_MQRankSum,Number=A,Type=Float,Description="Allele-specific Mapping Quality Rank Sum">
+##INFO=<ID=AS_QD,Number=A,Type=Float,Description="Allele-specific Variant Confidence/Quality by Depth">
+##INFO=<ID=AS_QUALapprox,Number=1,Type=String,Description="Allele-specific QUAL approximations">
+##INFO=<ID=AS_ReadPosRankSum,Number=A,Type=Float,Description="allele specific Z-score from Wilcoxon rank sum test of each Alt vs. Ref read position bias">
+##INFO=<ID=AS_SOR,Number=A,Type=Float,Description="Allele specific strand Odds Ratio of 2x|Alts| contingency table to detect allele specific strand bias">
+##INFO=<ID=AS_VarDP,Number=1,Type=String,Description="Allele-specific (informative) depth over variant genotypes -- including ref, RAW format">
+##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (informative and non-informative); some reads may have been filtered based on mapq etc.">
+##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
+##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
+##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
+##INFO=<ID=FractionInformativeReads,Number=1,Type=Float,Description="The fraction of informative reads out of the total reads">
+##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
+##INFO=<ID=LOD,Number=1,Type=Float,Description="Variant LOD score">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
+##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
+##INFO=<ID=MQ_DP,Number=1,Type=Integer,Description="Depth over variant samples for better MQ calculation (deprecated -- use RAW_MQandDP instead.)">
+##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
+##INFO=<ID=QUALapprox,Number=1,Type=Integer,Description="Sum of PL[0] values; used to approximate the QUAL score">
+##INFO=<ID=R2_5P_bias,Number=1,Type=Float,Description="Score based on mate bias and distance from 5 prime end">
+##INFO=<ID=RAW_GT_COUNT,Number=3,Type=Integer,Description="Counts of genotypes w.r.t. the reference allele in the following order: 0/0, 0/*, */*, i.e. all alts lumped together; for use in calculating excess heterozygosity">
+##INFO=<ID=RAW_MQandDP,Number=2,Type=Integer,Description="Raw data (sum of squared MQ and total depth) for improved RMS Mapping Quality calculation. Incompatible with deprecated RAW_MQ formulation.">
+##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
+##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
+##INFO=<ID=VarDP,Number=1,Type=Integer,Description="(informative) depth over variant genotypes">
+##contig=<ID=chrX,length=156040895>
+##reference=file:///seq/dragen/references/GRCh38dh/v3.7.8/reference.bin
+##source=ReblockGVCF
+##bcftools_viewVersion=1.19+htslib-1.19
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	haploid
+chrX	66780645	.	C	CT,<NON_REF>	65.55	.	AS_QUALapprox=|71|0;AS_VarDP=0|4|0;DP=9;MQ=216.86;QUALapprox=71;RAW_GT_COUNT=0,0,1;RAW_MQandDP=423254,9;VarDP=4	GT:AD:AF:DP:F1R2:F2R1:GQ:ICNT:MB:PL:SB:SPL	1:0,4,0:1,0:4:0,1,0:0,3,0:71:0,4:0,0,2,2:71,0,89:0,0,1,3:0,110
+chrX	66780646	.	T	TA,<NON_REF>	44.8	.	AS_QUALapprox=|50|0;AS_VarDP=13|8|0;DP=30;MQ=218.46;QUALapprox=50;RAW_GT_COUNT=0,1,0;RAW_MQandDP=1431743,30;VarDP=21	GT:AD:AF:DP:F1R2:F2R1:GQ:ICNT:MB:PL:SB:SPL	1:0,4,0:1,0:4:0,1,0:0,3,0:71:0,4:0,0,2,2:71,0,89:0,0,1,3:0,110
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/haploid.rb.g.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/haploid.rb.g.vcf.idx
new file mode 100644
index 00000000000..2acdf9a2707
Binary files /dev/null and b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/VCFComparator/haploid.rb.g.vcf.idx differ