diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
index 31c65252872c4ac3c01493bbf4ddc8abb6f5456e..5cbd73852e6a084a212a52052eebe1525bac3730 100644
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
@@ -111,6 +111,6 @@ class BwaMem(val root: Configurable) extends Bwa with Reference {
       required(reference) +
       required(R1) +
       optional(R2) +
-      " > " + required(output)
+      (if (outputAsStsout) "" else " > " + required(output))
   }
 }