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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
This commit is contained in:
corin 2010-11-18 21:02:15 +00:00
parent da1fe5bb37
commit 8dca5bd861
1 changed files with 4 additions and 2 deletions
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6
scala/qscript/fullCallingPipeline.q
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@ -206,6 +206,8 @@ class fullCallingPipeline extends QScript {
snps.jobOutputFile = new File(".queue/logs/SNPCalling/UnifiedGenotyper.out") snps.jobOutputFile = new File(".queue/logs/SNPCalling/UnifiedGenotyper.out")
snps.analysisName = base+"_SNP_calls" snps.analysisName = base+"_SNP_calls"
snps.input_file = bamFiles snps.input_file = bamFiles
snps.annotation ++= List("AlleleBalance")
snps.input_file = bamFiles
snps.group :+= "Standard" snps.group :+= "Standard"
snps.out = new File("SnpCalls", base+".vcf") snps.out = new File("SnpCalls", base+".vcf")
snps.standard_min_confidence_threshold_for_emitting = Some(10) 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.jobOutputFile = new File(".queue/logs/SNPCalling/HandFilter.out")
handFilter.variantVCF = masker.out handFilter.variantVCF = masker.out
handFilter.rodBind :+= RodBind("mask", "VCF", mergeIndels.out) handFilter.rodBind :+= RodBind("mask", "VCF", mergeIndels.out)
handFilter.filterName ++= List("StrandBias","QualByDepth","HomopolymerRun") handFilter.filterName ++= List("StrandBias","AlleleBalance","QualByDepth","HomopolymerRun")
handFilter.filterExpression ++= List("\"SB>=0.10\"","\"QD<5.0\"","\"HRun>=4\"") handFilter.filterExpression ++= List("\"SB>=0.10\"","\"AB>=0.75\"","\"QD<5.0\"","\"HRun>=4\"")
handFilter.out = swapExt("SnpCalls",annotated.out,".vcf",".handfiltered.vcf") handFilter.out = swapExt("SnpCalls",annotated.out,".vcf",".handfiltered.vcf")
handFilter.analysisName = base+"_HandFilter" handFilter.analysisName = base+"_HandFilter"