From 64325f978a8a542112bacddcc97f7c37957e9581 Mon Sep 17 00:00:00 2001
From: sajvanderzeeuw <s.a.j.van_der_zeeuw@lumc.nl>
Date: Mon, 18 Jan 2016 16:00:08 +0100
Subject: [PATCH] change sample name in varscan vcf
---
.../pipelines/shiva/variantcallers/VarscanCnsSingleSample.scala | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/VarscanCnsSingleSample.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/VarscanCnsSingleSample.scala
index 5cde45d4c..c4043d43b 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/VarscanCnsSingleSample.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/VarscanCnsSingleSample.scala
@@ -52,7 +52,7 @@ class VarscanCnsSingleSample(val root: Configurable) extends Variantcaller {
}
val varscan = new VarscanMpileup2cns(this)
- varscan.vcfSampleList = Some(sampleVcf)
+ varscan.vcfSampleList = Some(sampleFile)
add(mpileup | fixMpileup | varscan | new Bgzip(this) > sampleVcf)
add(Tabix(this, sampleVcf))
--
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