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 8bdd6ede13727d79165f6fcdd212ec55c38260ec..37ee728e62676c92d98bfc76f722aca4cbc24a93 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
@@ -619,7 +619,7 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi
     /** Picard CollectRnaSeqMetrics job */
     private def collectRnaSeqMetricsJob: CollectRnaSeqMetrics = {
       val job = new CollectRnaSeqMetrics(qscript)
-      job.input = alnFileDirty
+      job.input = alnFile
       job.output = createFile(".rna_metrics")
       job.refFlat = annotationRefFlat
       job.chartOutput = Option(createFile(".coverage_bias.pdf"))