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adding gold standard (full coverage) to the variant eval analysis output. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5721 348d0f76-0448-11de-a6fe-93d51630548a
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carneiro 2011-05-02 16:29:11 +00:00
parent f76e2791a9
commit a93a9ac663
1 changed files with 2 additions and 0 deletions
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2
scala/qscript/oneoffs/carneiro/downsampling.scala
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@ -54,6 +54,7 @@ class downsampling extends QScript {
val queueLogDir: String = ".qlog/" val queueLogDir: String = ".qlog/"
val outFile: String = "cov.out" val outFile: String = "cov.out"
val fullCoverageVCF = new File("/humgen/gsa-hpprojects/dev/carneiro/downsampling/analysis/fullcov/fullcov.F1.filtered.vcf")
def script = { def script = {
val nIntervals = math.min(200, countLines(targetIntervals)) val nIntervals = math.min(200, countLines(targetIntervals))
@ -126,6 +127,7 @@ class downsampling extends QScript {
this.stratificationModule ++= List("EvalRod", "CompRod", "Novelty") this.stratificationModule ++= List("EvalRod", "CompRod", "Novelty")
this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP) this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
this.rodBind :+= RodBind("eval", "VCF", inFile) this.rodBind :+= RodBind("eval", "VCF", inFile)
this.rodBind :+= RodBind("comp", "VCF", fullCoverageVCF)
this.out = outFile this.out = outFile
this.analysisName = outFile + "_VariantEval" this.analysisName = outFile + "_VariantEval"
this.jobName = queueLogDir + outFile this.jobName = queueLogDir + outFile