From c0e3874db095836e389d4ff7c277fb778a54c7b8 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Mon, 3 Jun 2013 14:34:29 -0400 Subject: [PATCH] Change the HC's phredScaledGlobalReadMismappingRate from 60 to 45, because Ryan and Mark told me to. --- .../sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java index a41b68e2c..24fd5901f 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java @@ -336,7 +336,7 @@ public class HaplotypeCaller extends ActiveRegionWalker, In */ @Advanced @Argument(fullName="phredScaledGlobalReadMismappingRate", shortName="globalMAPQ", doc="The global assumed mismapping rate for reads", required = false) - protected int phredScaledGlobalReadMismappingRate = 60; + protected int phredScaledGlobalReadMismappingRate = 45; @Advanced @Argument(fullName="maxNumHaplotypesInPopulation", shortName="maxNumHaplotypesInPopulation", doc="Maximum number of haplotypes to consider for your population. This number will probably need to be increased when calling organisms with high heterozygosity.", required = false)