diff --git a/java/src/org/broadinstitute/sting/playground/tools/SplitReads.java b/java/src/org/broadinstitute/sting/playground/tools/SplitReads.java
index 572d70edc..37cf040b8 100644
--- a/java/src/org/broadinstitute/sting/playground/tools/SplitReads.java
+++ b/java/src/org/broadinstitute/sting/playground/tools/SplitReads.java
@@ -123,6 +123,7 @@ public class SplitReads extends CommandLineProgram {
 
         }
 
+        inReader.close();
         for ( SAMFileWriter w : outWriters ) w.close();
 
         return 0;