diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/SortSam.scala b/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/SortSam.scala
index 9257cc7c2..b22bb2b59 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/SortSam.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/SortSam.scala
@@ -50,7 +50,7 @@ class SortSam extends org.broadinstitute.sting.queue.function.JavaCommandLineFun
   override def freezeFieldValues() {
     super.freezeFieldValues()
     if (outputIndex == null && output != null)
-      outputIndex = new File(output.getName.stripSuffix(".bam") + ".bai")
+      outputIndex = new File(output.getAbsolutePath.stripSuffix(".bam") + ".bai")
   }