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 269a88a6e..183597069 100644
--- a/java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java
@@ -95,10 +95,6 @@ public class VCFWriterStorage implements Storage<VCFWriterStorage>, VCFWriter {
         writer.close();
     }
 
-    public void flush() {
-        writer.flush();
-    }
-
     /**
      * Merges the stream backing up this temporary storage into the target.
      * @param target Target stream for the temporary storage.  May not be null.
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 cf479eec2..1a1981300 100755
--- a/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterStub.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterStub.java
@@ -184,10 +184,6 @@ 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