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Commit e430eb82 authored by Peter van 't Hof's avatar Peter van 't Hof
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Setting default for haplotypecaller

parent ec59d68a
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public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
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......@@ -36,6 +36,8 @@ trait ShivaTrait extends MultisampleMappingTrait with Reference with TargetRegio
Some(shiva)
}
override def defaults = Map("haplotypecaller" -> Map("stand_call_conf" -> 30, "stand_emit_conf" -> 0))
/** Method to make the variantcalling namespace of shiva */
def makeVariantcalling(multisample: Boolean = false): ShivaVariantcallingTrait with QScript = {
if (multisample) new ShivaVariantcalling(qscript) {
......
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