diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
index 0b4169ab138e87135640213e8c3bf224c04ce357..bb9575e1a2dcfb3a3403af7d23e8c0e8bab6be0e 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
@@ -52,6 +52,14 @@ class MarkDuplicates(val root: Configurable) extends Picard {
   @Argument(doc = "OPTICAL_DUPLICATE_PIXEL_DISTANCE", required = false)
   var opticalDuplicatePixelDistance: Option[Int] = config("opticalDuplicatePixelDistance")
 
+  @Output(doc = "Bam Index", required = true)
+  private var outputIndex: File = _
+  
+  override def afterGraph {
+    super.afterGraph
+    if (createIndex) outputIndex = new File(output.getAbsolutePath.stripSuffix(".bam") + ".bai")
+  }
+  
   override def commandLine = super.commandLine +
     repeat("INPUT=", input, spaceSeparated = false) +
     required("OUTPUT=", output, spaceSeparated = false) +
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
index 119d411e7e946e0764921e6d07bf1d5af81c4b6c..82f1fac3d6f53e586e19285aded171a5c7a9b31a 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
@@ -16,6 +16,14 @@ class SortSam(val root: Configurable) extends Picard {
   @Argument(doc = "Sort order of output file Required. Possible values: {unsorted, queryname, coordinate} ", required = true)
   var sortOrder: String = _
 
+  @Output(doc = "Bam Index", required = true)
+  private var outputIndex: File = _
+  
+  override def afterGraph {
+    super.afterGraph
+    if (createIndex) outputIndex = new File(output.getAbsolutePath.stripSuffix(".bam") + ".bai")
+  }
+  
   override def commandLine = super.commandLine +
     required("INPUT=", input, spaceSeparated = false) +
     required("OUTPUT=", output, spaceSeparated = false) +