diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala
index cff40a548b4545230010ae648ccf93d0081718d6..89b60840715afea2e8f8ff163ddbcd5cc5050ead 100644
--- a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala
+++ b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala
@@ -75,7 +75,7 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait {
       }
     }
 
-    override def keepMergedFiles: Boolean = config("keep_merged_files", default = false)
+    override def keepMergedFiles: Boolean = config("keep_merged_files", default = !useIndelRealigner)
 
     override def summarySettings = super.summarySettings + ("use_indel_realigner" -> useIndelRealigner)