diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLoci.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLoci.java
index 7cc847cd1..9b0d630ba 100644
--- a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLoci.java
+++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLoci.java
@@ -95,6 +95,9 @@ public class TraverseByLoci extends TraversalEngine {
 
         //printOnTraversalDone("loci", sum);
         walker.onTraversalDone(sum);
+
+        samReader.close();
+
         return sum;
     }