Commit f6bbd1b0 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added allSitePLs option

parent f66115cc
......@@ -131,7 +131,9 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
logger.warn("BamOutput is on, nct/threads is forced to set on 1, this option is only for debug")
}
this.memoryLimit = this.nct * 2
if (configContains("allSitePLs")) this.allSitePLs = config("allSitePLs")
// GVCF options
if (gvcfMode) {
this.emitRefConfidence = org.broadinstitute.gatk.tools.walkers.haplotypecaller.ReferenceConfidenceMode.GVCF
......
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