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biopet.biopet
Commit 0211653b authored by Peter van 't Hof's avatar Peter van 't Hof Committed by GitHub
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Revert "Remove default arguments"

parent 811fe4c2
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shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerGvcf.scala
View file @ 0211653b
......@@ -36,6 +36,11 @@ class HaplotypeCallerGvcf(val parent: Configurable) extends Variantcaller {
override def fixedValues = Map("haplotypecaller" -> Map("emitRefConfidence" -> "GVCF"))
override def defaults = Map("haplotypecaller" -> Map(
"variant_index_type" -> "LINEAR",
"variant_index_parameter" -> 128000)
)
def biopetScript() {
gVcfFiles = for ((sample, inputBam) <- inputBams) yield {
val hc = gatk.HaplotypeCaller(this, List(inputBam), new File(outputDir, sample + ".gvcf.vcf.gz"))
......
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