diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AssemblyBasedCallerUtils.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AssemblyBasedCallerUtils.java index 17a1334c04d..9c87e7e692a 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AssemblyBasedCallerUtils.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AssemblyBasedCallerUtils.java @@ -841,7 +841,7 @@ static Map> constructPhaseS final boolean compIsOnAllAltHaps = haplotypesWithComp.size() == totalAvailableHaplotypes; final Sets.SetView intersectionHaplotype = Sets.intersection(haplotypesWithCall, haplotypesWithComp); final int phaseReadsCount = intersectionHaplotype.stream().mapToInt(Haplotype::getWeakness).max().orElse(0); - final double phaseDiffusionRate = Math.pow(1.1 * Math.log10(Math.min(callDepth, compDepth)), 2) + 5; + final double phaseDiffusionRate = 2 * Math.log10(Math.min(callDepth, compDepth)) + 1; // For some high frequency complex long indels, that many reads not coverage the whole indels completely, // and variants will dispatch to different haplotypes, so we relax the conditions for phase set combination!