diff --git a/scala/qscript/oneoffs/fromer/phaseSamples.scala b/scala/qscript/oneoffs/fromer/phaseSamples.scala index d341c9950..4e06c5c7d 100644 --- a/scala/qscript/oneoffs/fromer/phaseSamples.scala +++ b/scala/qscript/oneoffs/fromer/phaseSamples.scala @@ -122,7 +122,7 @@ class CombineVariants(vcfsToCombine: List[File]) extends org.broadinstitute.stin this.variantMergeOptions = Some(org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.VariantMergeType.UNION) - this.out = new File(outputPhased) + this.out = outputPhased } }