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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
This commit is contained in:
corin 2010-11-18 20:22:05 +00:00
parent 79725f2d9c
commit da1fe5bb37
1 changed files with 2 additions and 2 deletions
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4
scala/qscript/fullCallingPipeline.q
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@ -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"