From 8dca5bd8613a3740d7167c2f92bb5ccc089fd5fc Mon Sep 17 00:00:00 2001 From: corin Date: Thu, 18 Nov 2010 21:02:15 +0000 Subject: [PATCH] Putting the annotation back in, both to the filters and to UG git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4709 348d0f76-0448-11de-a6fe-93d51630548a --- scala/qscript/fullCallingPipeline.q | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/scala/qscript/fullCallingPipeline.q b/scala/qscript/fullCallingPipeline.q index 50474cb7b..060cf588c 100755 --- a/scala/qscript/fullCallingPipeline.q +++ b/scala/qscript/fullCallingPipeline.q @@ -206,6 +206,8 @@ class fullCallingPipeline extends QScript { snps.jobOutputFile = new File(".queue/logs/SNPCalling/UnifiedGenotyper.out") snps.analysisName = base+"_SNP_calls" snps.input_file = bamFiles + snps.annotation ++= List("AlleleBalance") + snps.input_file = bamFiles snps.group :+= "Standard" snps.out = new File("SnpCalls", base+".vcf") snps.standard_min_confidence_threshold_for_emitting = Some(10) @@ -309,8 +311,8 @@ 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","QualByDepth","HomopolymerRun") - handFilter.filterExpression ++= List("\"SB>=0.10\"","\"QD<5.0\"","\"HRun>=4\"") + handFilter.filterName ++= List("StrandBias","AlleleBalance","QualByDepth","HomopolymerRun") + handFilter.filterExpression ++= List("\"SB>=0.10\"","\"AB>=0.75\"","\"QD<5.0\"","\"HRun>=4\"") handFilter.out = swapExt("SnpCalls",annotated.out,".vcf",".handfiltered.vcf") handFilter.analysisName = base+"_HandFilter"