diff --git a/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala b/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
index 1fd236b2429873143c9f10211dbd6d68e942e0d3..47774f2ea02bbe71c6fa2c63533f9098e5c73def 100644
--- a/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+++ b/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
@@ -201,7 +201,9 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
       bamFile = new File(outputDir + outputName + ".dedup.bam")
       add(MarkDuplicates(this, bamFiles, bamFile))
     } else if (skipMarkduplicates && chunking) bamFile = addMergeBam(bamFiles, new File(outputDir + outputName + ".bam"), outputDir)
-
+    
+    addAll(BamMetrics.apply(this, bamFile, outputDir + "metrics/").functions)
+    
     outputFiles += ("finalBamFile" -> bamFile)
   }