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Commit e66c1eec authored by Peter van 't Hof's avatar Peter van 't Hof Committed by GitHub
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Merge pull request #77 from biopet/revert-69-fix-BIOPET-654 

Revert "Remove default arguments"
parents 9c66f418 8ba7938f
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shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerGvcf.scala
View file @ e66c1eec
......@@ -60,6 +60,11 @@ 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 {
if (genderAwareCalling) {
......
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