diff --git a/scala/qscript/oneoffs/depristo/phaseSamples.scala b/scala/qscript/oneoffs/fromer/phaseSamples.scala similarity index 96% rename from scala/qscript/oneoffs/depristo/phaseSamples.scala rename to scala/qscript/oneoffs/fromer/phaseSamples.scala index d0def5f22..fddfb392e 100644 --- a/scala/qscript/oneoffs/depristo/phaseSamples.scala +++ b/scala/qscript/oneoffs/fromer/phaseSamples.scala @@ -117,9 +117,7 @@ class CombineVariants(vcfsToCombine: List[File]) extends org.broadinstitute.stin this.rodBind :+= RodBind(vcf.getName, "VCF", vcf) } - // add the master call - this.rodBind :+= RodBind("master", "VCF", masterCalls) - this.variantMergeOptions = Some(org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.VariantMergeType.MASTER) + this.variantMergeOptions = Some(org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.VariantMergeType.UNION) this.out = new File("phased.vcf") }