Commit f525d0f4 authored by Sander van der Zeeuw's avatar Sander van der Zeeuw
Browse files

Gentypegvcfs added freevar to avoid double annotation flag

parent a6e9c469
......@@ -10,7 +10,7 @@ import
import nl.lumc.sasc.biopet.utils.config.Configurable
class GenotypeGVCFs(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.GenotypeGVCFs with GatkGeneral {
annotation ++= config("annotation", default = Seq("FisherStrand", "QualByDepth", "ChromosomeCounts")).asStringList
annotation ++= config("annotation", default = Seq(), freeVar = false).asStringList
if (config.contains("dbsnp")) dbsnp = config("dbsnp")
if (config.contains("scattercount", "genotypegvcfs")) scatterCount = config("scattercount")
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