From 8ab6eee1cf875952cb1fdb85b132cf1b7ad498f9 Mon Sep 17 00:00:00 2001 From: carneiro Date: Tue, 1 Mar 2011 17:48:40 +0000 Subject: [PATCH] gold standard creates its own tranches and vcf files now. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5347 348d0f76-0448-11de-a6fe-93d51630548a --- .../qscript/core/MethodsDevelopmentCallingPipeline.scala | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/scala/qscript/core/MethodsDevelopmentCallingPipeline.scala b/scala/qscript/core/MethodsDevelopmentCallingPipeline.scala index 6bb3e03a3..fb449422b 100755 --- a/scala/qscript/core/MethodsDevelopmentCallingPipeline.scala +++ b/scala/qscript/core/MethodsDevelopmentCallingPipeline.scala @@ -75,10 +75,10 @@ class MethodsDevelopmentCallingPipeline extends QScript { val rawIndelVCF = new File(name + ".raw.indel.vcf") val filteredVCF = new File(name + ".filtered.vcf") val filteredIndelVCF = new File(name + ".filtered.indel.vcf") - val titvRecalibratedVCF = new File(name + ".titv.recalibrated.vcf") - val titvTranchesFile = new File(name + ".titv.tranches") val tsRecalibratedVCF = new File(name + ".ts.recalibrated.vcf") val tsTranchesFile = new File(name + ".ts.tranches") + val goldStandardTsRecalibratedVCF = new File(name + "goldStandard.ts.recalibrated.vcf") + val goldStandardTsTranchesFile = new File(name + "goldStandard.ts.tranches") val cutVCF = new File(name + ".cut.vcf") val evalFile = new File(name + ".snp.eval") val evalIndelFile = new File(name + ".indel.eval") @@ -302,8 +302,8 @@ class MethodsDevelopmentCallingPipeline extends QScript { this.rodBind :+= RodBind("dbsnp", "VCF", t.dbsnpFile) this.sm = Some(org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator.SelectionMetricType.TRUTH_SENSITIVITY) this.tranche ++= List("0.1", "0.5", "0.7", "1.0", "3.0", "5.0", "10.0", "100.0") - this.out = t.tsRecalibratedVCF - this.tranchesFile = t.tsTranchesFile + this.out = if ( goldStandard ) { t.goldStandardTsRecalibratedVCF } else { t.tsRecalibratedVCF } + this.tranchesFile = if ( goldStandard ) { t.goldStandardTsTranchesFile } else { t.tsTranchesFile } this.jobName = queueLogDir + t.name + ".nrs" this.trustAllPolymorphic = true }