Commit 0211653b authored by Peter van 't Hof's avatar Peter van 't Hof Committed by GitHub

Revert "Remove default arguments"

parent 811fe4c2
......@@ -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"))
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment