diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala
index 321cb8b9c5960936da9d8f5bcac0d2fdb9937627..a43fc4734852642b92e7924e2209073616197f6c 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala
@@ -36,5 +36,5 @@ class Bgzip(val root: Configurable) extends BiopetCommandLineFunction {
   def cmdLine = required(executable) +
     conditional(f, "-f") +
     " -c " + repeat(input) +
-    " > " + required(output)
+    (if (outputAsStsout) "" else " > " + required(output))
 }