Commit c3a86435 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Changed default stand_call_conf

parent 47c4429a
......@@ -25,12 +25,12 @@ class HaplotypeCaller(val root: Configurable) extends org.broadinstitute.gatk.qu
if (config("inputtype", default = "dna").getString == "rna") {
dontUseSoftClippedBases = config("dontusesoftclippedbases", default = true)
recoverDanglingHeads = config("recoverdanglingheads", default = true)
stand_call_conf = config("stand_call_conf", default = 20)
stand_call_conf = config("stand_call_conf", default = 0.0001)
stand_emit_conf = config("stand_emit_conf", default = 0)
} else {
dontUseSoftClippedBases = config("dontusesoftclippedbases", default = false)
recoverDanglingHeads = config("recoverdanglingheads", default = false)
stand_call_conf = config("stand_call_conf", default = 30)
stand_call_conf = config("stand_call_conf", default = 0.0001)
stand_emit_conf = config("stand_emit_conf", default = 0)
}
if (bamOutput != null && nct.getOrElse(1) > 1) {
......
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