diff --git a/scala/qscript/oneoffs/carneiro/downsampling.scala b/scala/qscript/oneoffs/carneiro/downsampling.scala index fcb0a8dc9..2b000f94a 100644 --- a/scala/qscript/oneoffs/carneiro/downsampling.scala +++ b/scala/qscript/oneoffs/carneiro/downsampling.scala @@ -54,6 +54,7 @@ class downsampling extends QScript { val queueLogDir: String = ".qlog/" val outFile: String = "cov.out" + val fullCoverageVCF = new File("/humgen/gsa-hpprojects/dev/carneiro/downsampling/analysis/fullcov/fullcov.F1.filtered.vcf") def script = { val nIntervals = math.min(200, countLines(targetIntervals)) @@ -126,6 +127,7 @@ class downsampling extends QScript { this.stratificationModule ++= List("EvalRod", "CompRod", "Novelty") this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP) this.rodBind :+= RodBind("eval", "VCF", inFile) + this.rodBind :+= RodBind("comp", "VCF", fullCoverageVCF) this.out = outFile this.analysisName = outFile + "_VariantEval" this.jobName = queueLogDir + outFile