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 62d004d63e3508a423471e757d2cdd3ad9bcf803..0eab05598fc49307439534a0845a03d415b863fd 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
@@ -132,8 +132,7 @@ class Gentrap(val root: Configurable) extends QScript
     ),
     // disable markduplicates since it may not play well with all aligners (this can still be overriden via config)
     "mapping" -> Map(
-      "skip_markduplicates" -> true,
-      "skip_metrics" -> true
+      "skip_markduplicates" -> true
     )
   )