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 37ee728e62676c92d98bfc76f722aca4cbc24a93..b095dc78ee6b9c7d28ba74ad63a6502bfab6f076 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)