From 74f90ad1d41df63d9c15e0d5c22b92867390c144 Mon Sep 17 00:00:00 2001
From: schaudge <yuanshenran@yeah.net>
Date: Mon, 9 Sep 2024 11:01:01 +0800
Subject: [PATCH] change phase diffusion calc.

---
 .../tools/walkers/haplotypecaller/AssemblyBasedCallerUtils.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

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<VariantContext, Triple<Integer, Integer, PhaseGroup>> constructPhaseS
                 final boolean compIsOnAllAltHaps = haplotypesWithComp.size() == totalAvailableHaplotypes;
                 final Sets.SetView<Haplotype> 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!