From b1276a9046ccac71f999aa497f9d4bb04a930c22 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 20 May 2014 09:23:18 +0200
Subject: [PATCH] - Added referenceFile to catVariants
---
gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala | 1 +
1 file changed, 1 insertion(+)
diff --git a/gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala b/gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala
index db20cb677..389e118b8 100644
--- a/gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala
+++ b/gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala
@@ -111,6 +111,7 @@ class Gatk(private var globalConfig: Config) extends QScript {
val catVariants = new CatVariants()
catVariants.variant = Seq(snpApplyRecalibration.out,indelApplyRecalibration.out)
catVariants.outputFile = swapExt(genotypeGVCFs.out,".vcf",".recal.vcf")
+ catVariants.reference = referenceFile
add(catVariants)
} else logger.warn("No gVCFs to genotype")
--
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