diff --git a/bam-metrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala b/bam-metrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
index d0ec70ad7889ce00a45e0ced22c5bfc99e4eff5e..e2b0452a37782a71b8f20ff244c0703e984b098c 100644
--- a/bam-metrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
+++ b/bam-metrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
@@ -29,6 +29,11 @@ class BamMetrics(val root: Configurable) extends QScript with BiopetQScript {
     for (file <- configfiles) globalConfig.loadConfigFile(file)
     if (outputDir == null) throw new IllegalStateException("Missing Output directory on BamMetrics module")
     else if (!outputDir.endsWith("/")) outputDir += "/"
+    if (configContains("targetBed")) {
+      for (file <- config("targetBed").getList) {
+        bedFiles +:= new File(file.toString)
+      }
+    }
   }
 
   def biopetScript() {