Commit ef67b6a8 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Change defaults

parent 56df29e7
......@@ -22,9 +22,10 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
var outputSnps: FastaOutput = _
}
defaults ++= Map("ploidy" -> 1, "use_haplotypecaller" -> false, "use_unifiedgenotyper" -> true)
defaults ++= Map("ploidy" -> 1, "use_haplotypecaller" -> false, "use_unifiedgenotyper" -> true, "joint_variantcalling" -> true)
var gatkPipeline: GatkPipeline = _
gatkPipeline.jointVariantcalling = true
def init() {
gatkPipeline = new GatkPipeline(this)
......
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