From 6c7c75a7027b4f38c5035e0d46532972dde483e7 Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Sun, 8 Mar 2015 12:34:24 +0100
Subject: [PATCH] Default to not using MarkDuplicates PG tag as it creates
conflicts when merging BAM files
---
.../scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala | 4 ++++
1 file changed, 4 insertions(+)
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
index 37ee728e6..b095dc78e 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
@@ -87,6 +87,10 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi
"novelsplicing" -> 1,
"batch" -> 4,
"format" -> "sam"
+ ),
+ // avoid conflicts when merging since the MarkDuplicate tags often cause merges to fail
+ "picard" -> Map (
+ "programrecordid" -> "null"
)
), super.defaults)
--
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