From f525d0f4be97f814c7e54f73726ade084e57ab02 Mon Sep 17 00:00:00 2001
From: sajvanderzeeuw <s.a.j.van_der_zeeuw@lumc.nl>
Date: Tue, 13 Oct 2015 11:55:03 +0200
Subject: [PATCH] Gentypegvcfs added freevar to avoid double annotation flag
---
.../lumc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala
index 5bd36585d..e347ebf47 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala
@@ -10,7 +10,7 @@ import java.io.File
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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