zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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
This commit is contained in:
carneiro 2011-03-01 17:48:40 +00:00
parent 3c7ae0d1a6
commit 8ab6eee1cf
1 changed files with 4 additions and 4 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

8
scala/qscript/core/MethodsDevelopmentCallingPipeline.scala
View File

@ -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
}