diff --git a/java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java b/java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java
index f61540d66..269a88a6e 100644
--- a/java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java
@@ -93,7 +93,11 @@ public class VCFWriterStorage implements Storage<VCFWriterStorage>, VCFWriter {
      */
     public void close() {
         writer.close();
-    }    
+    }
+
+    public void flush() {
+        writer.flush();
+    }
 
     /**
      * Merges the stream backing up this temporary storage into the target.
diff --git a/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterStub.java b/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterStub.java
index 1a1981300..cf479eec2 100755
--- a/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterStub.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterStub.java
@@ -184,6 +184,10 @@ public class VCFWriterStub implements Stub<VCFWriter>, VCFWriter {
         outputTracker.getStorage(this).close();
     }
 
+    public void flush() {
+        outputTracker.getStorage(this).flush();
+    }
+
     /**
      * Gets a string representation of this object.
      * @return