diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/IndexingVariantContextWriter.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/IndexingVariantContextWriter.java
index 4f577fbcf..df0feda8b 100644
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/IndexingVariantContextWriter.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/IndexingVariantContextWriter.java
@@ -159,4 +159,10 @@ final class PositionalOutputStream extends OutputStream {
     }
 
     public final long getPosition() { return position; }
+
+    @Override
+    public void close() throws IOException {
+        super.close();
+        out.close();
+    }
 }
\ No newline at end of file