From 74123531d7a79ad15eefd704cbcedd1d6407c4e1 Mon Sep 17 00:00:00 2001 From: David Benjamin Date: Thu, 7 Dec 2023 00:09:52 -0500 Subject: [PATCH] restpored the log(1/3) for SNP het prior --- .../haplotypecaller/HaplotypeCallerGenotypingEngine.java | 2 +- .../hellbender/utils/genotyper/GenotypePriorCalculator.java | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java index fc65447155a..dc0ec758683 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java @@ -395,7 +395,7 @@ private OverlapDetector computeHaploGenotypingResults(All final List allEvents = jdHaplotypes.stream().flatMap(haplotype -> haplotype.getEventMap().getEvents().stream()).distinct().toList(); final Map 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 index 9512d9dd138..4b4130aaa17 100644 --- 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;