Commit ac9315e7 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added normalize option to shiva

parent 73088af2
......@@ -19,6 +19,7 @@ import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.core.{ Reference, SampleLibraryTag }
import nl.lumc.sasc.biopet.extensions.gatk.{ CombineVariants, GenotypeConcordance }
import nl.lumc.sasc.biopet.extensions.tools.VcfStats
import nl.lumc.sasc.biopet.extensions.vt.VtNormalize
import nl.lumc.sasc.biopet.pipelines.bammetrics.TargetRegions
import nl.lumc.sasc.biopet.pipelines.shiva.variantcallers._
import nl.lumc.sasc.biopet.utils.{ BamUtils, Logging }
......@@ -86,9 +87,15 @@ trait ShivaVariantcallingTrait extends SummaryQScript
for (caller <- callers) {
caller.inputBams = inputBams
add(caller)
cv.addInput(caller.outputFile, caller.name)
addStats(caller.outputFile, caller.name)
val normalize: Boolean = config("execute_vt_normalize", default = false)
if (normalize) {
val vt = new VtNormalize(this)
vt.inputVcf = caller.outputFile
vt.outputVcf = swapExt(caller.outputDir, caller.outputFile, ".vcf.gz", ".normaize.vcf.gz")
add(vt)
cv.addInput(vt.outputVcf, caller.name)
} else cv.addInput(caller.outputFile, caller.name)
}
add(cv)
......
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