restpored the log(1/3) for SNP het prior

broadinstitute · Dec 7, 2023 · 7412353 · 7412353
1 parent 4817f53
commit 7412353
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/...adinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java b/...adinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java
@@ -395,7 +395,7 @@ private OverlapDetector<HaploGenotypingResult> computeHaploGenotypingResults(All
                 final List<Event> allEvents = jdHaplotypes.stream().flatMap(haplotype -> haplotype.getEventMap().getEvents().stream()).distinct().toList();
                 final Map<Event, Double> log10EventHetPriors = new HashMap<>();
                 for (final Event event : allEvents) {
-                    final double log10SNPHetPrior = Math.log10(snpHeterozygosity);
+                    final double log10SNPHetPrior = Math.log10(snpHeterozygosity) - GenotypePriorCalculator.LOG10_SNP_NORMALIZATION_CONSTANT;
                     if (event.isSNP()) {
                         log10EventHetPriors.put(event, log10SNPHetPrior);
                     } else {

diff --git a/src/main/java/org/broadinstitute/hellbender/utils/genotyper/GenotypePriorCalculator.java b/src/main/java/org/broadinstitute/hellbender/utils/genotyper/GenotypePriorCalculator.java
@@ -39,7 +39,7 @@ private enum AlleleType {
 
     // A snp can go to 3 different bases (standard-nucs - 1), so we normalize SNP lks accordingly. Here is the
     // log10 constant used for that:
-    private static final double LOG10_SNP_NORMALIZATION_CONSTANT =
+    public static final double LOG10_SNP_NORMALIZATION_CONSTANT =
             Math.log10(Nucleotide.STANDARD_BASES.size() - 1);
 
     private final double[] hetValues;