From da1fe5bb37199f533fe64d278d7a2c6e406989e4 Mon Sep 17 00:00:00 2001 From: corin Date: Thu, 18 Nov 2010 20:22:05 +0000 Subject: [PATCH] Removing the AB filter given that we don't have that in the VCF anymore git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4708 348d0f76-0448-11de-a6fe-93d51630548a --- scala/qscript/fullCallingPipeline.q | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/scala/qscript/fullCallingPipeline.q b/scala/qscript/fullCallingPipeline.q index 54e8973c0..50474cb7b 100755 --- a/scala/qscript/fullCallingPipeline.q +++ b/scala/qscript/fullCallingPipeline.q @@ -309,8 +309,8 @@ class fullCallingPipeline extends QScript { handFilter.jobOutputFile = new File(".queue/logs/SNPCalling/HandFilter.out") handFilter.variantVCF = masker.out handFilter.rodBind :+= RodBind("mask", "VCF", mergeIndels.out) - handFilter.filterName ++= List("StrandBias","AlleleBalance","QualByDepth","HomopolymerRun") - handFilter.filterExpression ++= List("\"SB>=0.10\"","\"AB>=0.75\"","\"QD<5.0\"","\"HRun>=4\"") + handFilter.filterName ++= List("StrandBias","QualByDepth","HomopolymerRun") + handFilter.filterExpression ++= List("\"SB>=0.10\"","\"QD<5.0\"","\"HRun>=4\"") handFilter.out = swapExt("SnpCalls",annotated.out,".vcf",".handfiltered.vcf") handFilter.analysisName = base+"_HandFilter"