Commit f6841e2c authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix combine variants

parent 77d06f6e
......@@ -39,8 +39,8 @@ class CombineVariants(val root: Configurable) extends Gatk {
override def commandLine = super.commandLine +
(for (file <- inputFiles) yield {
inputMap.get(file) match {
case Some(name) => required("--variant:" + name, file)
case _ => required("--variant", file)
case Some(name) => required("-V:" + name, file)
case _ => required("-V", file)
}
}).mkString +
required("-o", outputFile) +
......
......@@ -34,12 +34,14 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag {
def finalFile = new File(outputDir, namePrefix + "final.vcf.gz")
def biopetScript: Unit = {
val callers = usedCallers
val callers = usedCallers.sortBy(_.prio)
val cv = new CombineVariants(qscript)
cv.outputFile = finalFile
cv.setKey = "VariantCaller"
for (caller <- callers.sortBy(_.prio)) {
cv.genotypeMergeOptions = Some("PRIORITIZE")
cv.rodPriorityList = callers.map(_.name).mkString(",")
for (caller <- callers) {
caller.addJobs()
cv.addInput(caller.outputFile, caller.name)
}
......@@ -99,6 +101,7 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag {
val cv = new CombineVariants(qscript)
cv.inputFiles = rawFiles
cv.outputFile = outputFile
cv.setKey = "null"
add(cv)
}
}
......
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