VS-1007 - Use default names for VQSR-Lite generated code. (#8412)

* Remove some unused VCF header fields from ExtractFeatures
* Renaming VQS_SENS and related constants back to 'CALIBRATION_SENSITIVITY' (as it is named by VQSR Lite) to reduce confusion.
* Update dockers and override jar
* Updated truth path for integration tests

scripts/variantstore/wdl/GvsCreateFilterSet.wdl

@@ -293,7 +293,7 @@ task ExtractFilterTask {
   >>>
 
   runtime {
-    docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_2023_07_02_e90d90e00615dcbd9a71d4301fdc04fe2fe155fc"
+    docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_2023_07_12"
     memory: "7 GB"
     disks: "local-disk 10 HDD"
     bootDiskSizeGb: 15
@@ -355,7 +355,7 @@ task PopulateFilterSetSites {
   >>>
 
   runtime {
-    docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_2023_07_02_e90d90e00615dcbd9a71d4301fdc04fe2fe155fc"
+    docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_2023_07_12"
     memory: "3500 MB"
     disks: "local-disk 200 HDD"
     bootDiskSizeGb: 15

scripts/variantstore/wdl/GvsExtractCallset.wdl

@@ -354,7 +354,7 @@ task ExtractTask {
     echo ~{interval_index},${OUTPUT_FILE_DEST},${OUTPUT_FILE_BYTES},${OUTPUT_FILE_INDEX_DEST},${OUTPUT_FILE_INDEX_BYTES} >> manifest.txt
   >>>
   runtime {
-    docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_2023_07_02_e90d90e00615dcbd9a71d4301fdc04fe2fe155fc"
+    docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_2023_07_12"
     memory: "12 GB"
     disks: "local-disk 150 HDD"
     bootDiskSizeGb: 15

scripts/variantstore/wdl/GvsImportGenomes.wdl

@@ -323,7 +323,7 @@ task LoadData {
   >>>
 
   runtime {
-    docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_2023_07_02_e90d90e00615dcbd9a71d4301fdc04fe2fe155fc"
+    docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_2023_07_12"
     maxRetries: load_data_maxretries
     memory: "3.75 GB"
     disks: "local-disk 50 HDD"

scripts/variantstore/wdl/GvsJointVariantCalling.wdl

@@ -38,8 +38,8 @@ workflow GvsJointVariantCalling {
       Int SNP_VQSR_CLASSIC_max_gaussians_override = 6
       Int SNP_VQSR_CLASSIC_mem_gb_override = ""
     }
-    # This is the most updated snapshot of the code as of July 2, 2023
-    File gatk_override = "gs://gvs_quickstart_storage/jars/gatk-package-4.2.0.0-724-gf478fb2-SNAPSHOT-local.jar"
+    # This is the most updated snapshot of the code as of July 12, 2023
+    File gatk_override = "gs://gvs_quickstart_storage/jars/gatk-package-4.2.0.0-727-g950da0b-SNAPSHOT-local.jar"
     File interval_list = "gs://gcp-public-data--broad-references/hg38/v0/wgs_calling_regions.hg38.noCentromeres.noTelomeres.interval_list"
 
     File interval_weights_bed = "gs://broad-public-datasets/gvs/weights/gvs_vet_weights_1kb.bed"

scripts/variantstore/wdl/GvsQuickstartIntegration.wdl

@@ -34,7 +34,7 @@ workflow GvsQuickstartIntegration {
     }
 
     File full_interval_list = "gs://gcp-public-data--broad-references/hg38/v0/wgs_calling_regions.hg38.noCentromeres.noTelomeres.interval_list"
-    File expected_output_prefix = "gs://gvs-internal-quickstart/integration/2023-06-06-quicker/"
+    File expected_output_prefix = "gs://gvs-internal-quickstart/integration/2023-07-12-quicker/"
 
     call FilterIntervalListChromosomes {
         input:

scripts/variantstore/wdl/GvsUtils.wdl

@@ -41,7 +41,7 @@ task MergeVCFs {
   }
 
   runtime {
-    docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_2023_07_02_e90d90e00615dcbd9a71d4301fdc04fe2fe155fc"
+    docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_2023_07_12"
     preemptible: select_first([preemptible_tries, 3])
     memory: "3 GiB"
     disks: "local-disk ~{disk_size} HDD"
@@ -127,7 +127,7 @@ task SplitIntervals {
   >>>
 
   runtime {
-    docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_2023_07_02_e90d90e00615dcbd9a71d4301fdc04fe2fe155fc"
+    docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_2023_07_12"
     bootDiskSizeGb: 15
     memory: "~{disk_memory} GB"
     disks: "local-disk ~{disk_size} HDD"
@@ -934,7 +934,7 @@ task PopulateFilterSetInfo {
   >>>
 
   runtime {
-    docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_2023_07_02_e90d90e00615dcbd9a71d4301fdc04fe2fe155fc"
+    docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_2023_07_12"
     memory: "3500 MB"
     disks: "local-disk 250 HDD"
     bootDiskSizeGb: 15

scripts/variantstore/wdl/GvsVQSRClassic.wdl

@@ -362,7 +362,7 @@ task GatherTranches {
     bootDiskSizeGb: 15
     disks: "local-disk " + disk_size + " HDD"
     preemptible: 1
-    docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_2023_07_02_e90d90e00615dcbd9a71d4301fdc04fe2fe155fc"
+    docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_2023_07_12"
   }
 
   output {
@@ -565,7 +565,7 @@ task PopulateFilterSetTranches {
   >>>
 
   runtime {
-    docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_2023_07_02_e90d90e00615dcbd9a71d4301fdc04fe2fe155fc"
+    docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_2023_07_12"
     memory: "3500 MB"
     disks: "local-disk 200 HDD"
     bootDiskSizeGb: 15

src/main/java/org/broadinstitute/hellbender/tools/gvs/common/CommonCode.java

@@ -1,18 +1,13 @@
 package org.broadinstitute.hellbender.tools.gvs.common;
 
-import htsjdk.samtools.SAMSequenceDictionary;
 import htsjdk.variant.variantcontext.Allele;
 import htsjdk.variant.variantcontext.VariantContext;
-import htsjdk.variant.vcf.*;
+import htsjdk.variant.vcf.VCFConstants;
 import org.apache.commons.lang.StringUtils;
 import org.broadinstitute.hellbender.utils.genotyper.IndexedAlleleList;
-import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants;
-import org.broadinstitute.hellbender.utils.variant.GATKVCFHeaderLines;
 
 import java.util.ArrayList;
-import java.util.HashSet;
 import java.util.List;
-import java.util.Set;
 import java.util.stream.Collectors;
 
 //TODO rename this or get rid of it. a place holder for now
@@ -53,92 +48,6 @@ public static String getGTString(final VariantContext variant) {
         return StringUtils.join(gsStrings, separator);
     }
 
-    public static VCFHeader generateVcfHeader(Set<String> sampleNames,
-                                              final SAMSequenceDictionary sequenceDictionary,
-                                              final Set<VCFHeaderLine> extraHeaders) {
-        final Set<VCFHeaderLine> headerLines = new HashSet<>();
-
-        headerLines.addAll( getEvoquerVcfHeaderLines() );
-        headerLines.addAll( extraHeaders );
-//        headerLines.addAll( defaultHeaderLines );
-
-        final VCFHeader header = new VCFHeader(headerLines, sampleNames);
-        header.setSequenceDictionary(sequenceDictionary);
-
-        return header;
-    }
-
-    // TODO is this specific for cohort extract? if so name it such
-    public static Set<VCFHeaderLine> getEvoquerVcfHeaderLines() {
-        final Set<VCFHeaderLine> headerLines = new HashSet<>();
-
-        // TODO: Get a list of all possible values here so that we can make sure they're in the VCF Header!
-
-        // Add standard VCF fields first:
-        VCFStandardHeaderLines.addStandardInfoLines( headerLines, true,
-                VCFConstants.STRAND_BIAS_KEY,
-                VCFConstants.DEPTH_KEY,
-                VCFConstants.RMS_MAPPING_QUALITY_KEY,
-                VCFConstants.ALLELE_COUNT_KEY,
-                VCFConstants.ALLELE_FREQUENCY_KEY,
-                VCFConstants.ALLELE_NUMBER_KEY,
-                VCFConstants.END_KEY
-        );
-
-        VCFStandardHeaderLines.addStandardFormatLines(headerLines, true,
-                VCFConstants.GENOTYPE_KEY,
-                VCFConstants.GENOTYPE_QUALITY_KEY,
-                VCFConstants.DEPTH_KEY,
-                VCFConstants.GENOTYPE_PL_KEY,
-                VCFConstants.GENOTYPE_ALLELE_DEPTHS
-        );
-
-        headerLines.add(GATKVCFHeaderLines.getFormatLine(GATKVCFConstants.REFERENCE_GENOTYPE_QUALITY));
-
-        headerLines.add(GATKVCFHeaderLines.getFormatLine(GATKVCFConstants.HAPLOTYPE_CALLER_PHASING_GT_KEY));
-        headerLines.add(GATKVCFHeaderLines.getFormatLine(GATKVCFConstants.HAPLOTYPE_CALLER_PHASING_ID_KEY));
-
-        headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_RAW_RMS_MAPPING_QUALITY_KEY));
-        headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_RMS_MAPPING_QUALITY_KEY));
-
-        headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_RAW_MAP_QUAL_RANK_SUM_KEY));
-        headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_MAP_QUAL_RANK_SUM_KEY));
-
-        headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_RAW_QUAL_APPROX_KEY));
-        headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.RAW_QUAL_APPROX_KEY));
-
-        headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_RAW_READ_POS_RANK_SUM_KEY));
-        headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_READ_POS_RANK_SUM_KEY));
-
-        headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_SB_TABLE_KEY));
-        headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.SB_TABLE_KEY));
-
-        headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_VQS_LOD_KEY));
-        headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_YNG_STATUS_KEY));
-
-        headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_VARIANT_DEPTH_KEY));
-        headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.VARIANT_DEPTH_KEY));
-
-        headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_STRAND_ODDS_RATIO_KEY));
-
-        headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_FISHER_STRAND_KEY));
-
-        headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_QUAL_BY_DEPTH_KEY));
-        headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.QUAL_BY_DEPTH_KEY));
-
-        headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.EXCESS_HET_KEY));
-
-        headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.SB_TABLE_KEY));
-
-        headerLines.add(GATKVCFHeaderLines.getFilterLine(GATKVCFConstants.NAY_FROM_YNG));
-        headerLines.add(GATKVCFHeaderLines.getFilterLine(GATKVCFConstants.EXCESS_HET_KEY));
-
-        headerLines.add(GATKVCFHeaderLines.getFilterLine(GATKVCFConstants.EXCESS_ALLELES));
-        headerLines.add(GATKVCFHeaderLines.getFilterLine(GATKVCFConstants.NO_HQ_GENOTYPES));
-
-        return headerLines;
-    }
-
     public enum OutputType {
         TSV,
         ORC,

src/main/java/org/broadinstitute/hellbender/tools/gvs/common/FilterSensitivityTools.java

@@ -123,12 +123,6 @@ public static VCFHeaderLine getVqsLodHeader(Double vqsLodThreshold, String model
                 "Site failed " + model + " model VQSLOD cutoff of " + vqsLodThreshold.toString());
     }
 
-    public static VCFHeaderLine getExcessAllelesHeader(int excessAllelesThreshold, String model) {
-        // should there be a gate for max or min excessAllelesThreshold value?
-        return new VCFFilterHeaderLine(GATKVCFConstants.VQSR_FAILURE_PREFIX + model,
-            "Site failed " + model + " model excess allele cutoff (" + excessAllelesThreshold + ")");
-    }
-
     public static VCFHeaderLine getTruthSensitivityHeader(Double truthSensitivityThreshold, Double vqsLodThreshold, String model) {
         if (truthSensitivityThreshold == null) {  // at this point, we know that all vqsr threshold inputs are null, so use defaults
             truthSensitivityThreshold = GATKVCFConstants.SNP.contains(model) ? DEFAULT_TRUTH_SENSITIVITY_THRESHOLD_SNPS : DEFAULT_TRUTH_SENSITIVITY_THRESHOLD_INDELS;

src/main/java/org/broadinstitute/hellbender/tools/gvs/extract/ExtractCohort.java

@@ -316,22 +316,22 @@ protected void onStartup() {
                     extraHeaderLines.add(FilterSensitivityTools.getTruthSensitivityHeader(truthSensitivityINDELThreshold, vqsLodINDELThreshold, GATKVCFConstants.INDEL));
                 }
             } else {
-                extraHeaderLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_VQS_SENS_KEY));
+                extraHeaderLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.CALIBRATION_SENSITIVITY_KEY));
                 if (truthSensitivitySNPThreshold == null) {
                     truthSensitivitySNPThreshold = FilterSensitivityTools.DEFAULT_TRUTH_SENSITIVITY_THRESHOLD_SNPS;
                 }
                 truthSensitivitySNPThreshold /= 100.0;
-                logger.info("Passing all SNP variants with calibration_sensitivity < " + truthSensitivitySNPThreshold);
+                logger.info("Passing all SNP variants with " + GATKVCFConstants.CALIBRATION_SENSITIVITY_KEY + " < " + truthSensitivitySNPThreshold);
 
                 if (truthSensitivityINDELThreshold == null) {
                     truthSensitivityINDELThreshold = FilterSensitivityTools.DEFAULT_TRUTH_SENSITIVITY_THRESHOLD_INDELS;
                 }
                 truthSensitivityINDELThreshold /= 100.0;
-                logger.info("Passing all INDEL variants with calibration_sensitivity < " + truthSensitivityINDELThreshold);
+                logger.info("Passing all INDEL variants with " + GATKVCFConstants.CALIBRATION_SENSITIVITY_KEY + " < " + truthSensitivityINDELThreshold);
 
-                extraHeaderLines.add(new VCFFilterHeaderLine(GATKVCFConstants.VQS_SENS_FAILURE_SNP,
+                extraHeaderLines.add(new VCFFilterHeaderLine(GATKVCFConstants.CALIBRATION_SENSITIVITY_FAILURE_SNP,
                         "Site failed SNP model calibration sensitivity cutoff (" + truthSensitivitySNPThreshold.toString() + ")"));
-                extraHeaderLines.add(new VCFFilterHeaderLine(GATKVCFConstants.VQS_SENS_FAILURE_INDEL,
+                extraHeaderLines.add(new VCFFilterHeaderLine(GATKVCFConstants.CALIBRATION_SENSITIVITY_FAILURE_INDEL,
                         "Site failed INDEL model calibration sensitivity cutoff (" + truthSensitivityINDELThreshold.toString() + ")"));
             }
         }

src/main/java/org/broadinstitute/hellbender/tools/gvs/extract/ExtractCohortLiteEngine.java

@@ -32,15 +32,15 @@ String getVQScoreFieldName() {
     }
 
     String getAlleleSpecificVQSScoreKey() {
-        return GATKVCFConstants.AS_VQS_SENS_KEY;
+        return GATKVCFConstants.CALIBRATION_SENSITIVITY_KEY;
     }
 
     String getVqScoreSNPFailureFilterName() {
-        return GATKVCFConstants.VQS_SENS_FAILURE_SNP;
+        return GATKVCFConstants.CALIBRATION_SENSITIVITY_FAILURE_SNP;
     }
 
     String getVqScoreINDELFailureFilterName() {
-        return GATKVCFConstants.VQS_SENS_FAILURE_INDEL;
+        return GATKVCFConstants.CALIBRATION_SENSITIVITY_FAILURE_INDEL;
     }
 
     public ExtractCohortLiteEngine(final String projectID,

src/main/java/org/broadinstitute/hellbender/tools/gvs/filtering/ExtractFeatures.java

@@ -1,8 +1,11 @@
 package org.broadinstitute.hellbender.tools.gvs.filtering;
 
+import htsjdk.samtools.SAMSequenceDictionary;
 import htsjdk.variant.variantcontext.writer.VariantContextWriter;
+import htsjdk.variant.vcf.VCFConstants;
 import htsjdk.variant.vcf.VCFHeader;
 import htsjdk.variant.vcf.VCFHeaderLine;
+import htsjdk.variant.vcf.VCFStandardHeaderLines;
 import org.broadinstitute.barclay.argparser.Argument;
 import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
 import org.broadinstitute.barclay.help.DocumentedFeature;
@@ -136,12 +139,9 @@ protected void onStartup() {
         sampleList = new SampleList(sampleTableName, sampleFileName, projectID, printDebugInformation, "extract-features");
 
         Set<VCFHeaderLine> extraHeaderLines = new HashSet<>();
-        extraHeaderLines.add(
-                FilterSensitivityTools.getExcessAllelesHeader(excessAllelesThreshold, GATKVCFConstants.EXCESS_ALLELES));
-
         extraHeaderLines.add(GATKVCFHeaderLines.getFilterLine(GATKVCFConstants.LOW_QUAL_FILTER_NAME));
 
-        VCFHeader header = CommonCode.generateVcfHeader(
+        VCFHeader header = generateVcfHeader(
                 new HashSet<>(), reference.getSequenceDictionary(), extraHeaderLines);
 
         vcfWriter = createVCFWriter(IOUtils.getPath(outputVcfPathString));
@@ -216,4 +216,79 @@ protected void onShutdown() {
         }
     }
 
+    private static VCFHeader generateVcfHeader(Set<String> sampleNames,
+                                              final SAMSequenceDictionary sequenceDictionary,
+                                              final Set<VCFHeaderLine> extraHeaders) {
+        final Set<VCFHeaderLine> headerLines = new HashSet<>();
+
+        headerLines.addAll( getEvoquerVcfHeaderLines() );
+        headerLines.addAll( extraHeaders );
+        final VCFHeader header = new VCFHeader(headerLines, sampleNames);
+        header.setSequenceDictionary(sequenceDictionary);
+
+        return header;
+    }
+
+    private static Set<VCFHeaderLine> getEvoquerVcfHeaderLines() {
+        final Set<VCFHeaderLine> headerLines = new HashSet<>();
+        // Add standard VCF fields first:
+        VCFStandardHeaderLines.addStandardInfoLines( headerLines, true,
+                VCFConstants.STRAND_BIAS_KEY,
+                VCFConstants.DEPTH_KEY,
+                VCFConstants.RMS_MAPPING_QUALITY_KEY,
+                VCFConstants.ALLELE_COUNT_KEY,
+                VCFConstants.ALLELE_FREQUENCY_KEY,
+                VCFConstants.ALLELE_NUMBER_KEY,
+                VCFConstants.END_KEY
+        );
+
+        VCFStandardHeaderLines.addStandardFormatLines(headerLines, true,
+                VCFConstants.GENOTYPE_KEY,
+                VCFConstants.GENOTYPE_QUALITY_KEY,
+                VCFConstants.DEPTH_KEY,
+                VCFConstants.GENOTYPE_PL_KEY,
+                VCFConstants.GENOTYPE_ALLELE_DEPTHS
+        );
+
+        headerLines.add(GATKVCFHeaderLines.getFormatLine(GATKVCFConstants.REFERENCE_GENOTYPE_QUALITY));
+
+        headerLines.add(GATKVCFHeaderLines.getFormatLine(GATKVCFConstants.HAPLOTYPE_CALLER_PHASING_GT_KEY));
+        headerLines.add(GATKVCFHeaderLines.getFormatLine(GATKVCFConstants.HAPLOTYPE_CALLER_PHASING_ID_KEY));
+
+        headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_RAW_RMS_MAPPING_QUALITY_KEY));
+        headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_RMS_MAPPING_QUALITY_KEY));
+
+        headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_RAW_MAP_QUAL_RANK_SUM_KEY));
+        headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_MAP_QUAL_RANK_SUM_KEY));
+
+        headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_RAW_QUAL_APPROX_KEY));
+        headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.RAW_QUAL_APPROX_KEY));
+
+        headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_RAW_READ_POS_RANK_SUM_KEY));
+        headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_READ_POS_RANK_SUM_KEY));
+
+        headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_SB_TABLE_KEY));
+        headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.SB_TABLE_KEY));
+
+        headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_VARIANT_DEPTH_KEY));
+        headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.VARIANT_DEPTH_KEY));
+
+        headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_STRAND_ODDS_RATIO_KEY));
+
+        headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_FISHER_STRAND_KEY));
+
+        headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_QUAL_BY_DEPTH_KEY));
+        headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.QUAL_BY_DEPTH_KEY));
+
+        headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.EXCESS_HET_KEY));
+
+        headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.SB_TABLE_KEY));
+
+        headerLines.add(GATKVCFHeaderLines.getFilterLine(GATKVCFConstants.EXCESS_HET_KEY));
+        headerLines.add(GATKVCFHeaderLines.getFilterLine(GATKVCFConstants.EXCESS_ALLELES));
+        headerLines.add(GATKVCFHeaderLines.getFilterLine(GATKVCFConstants.NO_HQ_GENOTYPES));
+
+        return headerLines;
+    }
+
 }