diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java
index ac46c2961..4e2c34510 100644
--- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java
@@ -99,7 +99,8 @@ public class VCFGenotypeWriterAdapter implements GenotypeWriter {
     /** finish writing, closing any open files. */
     @Override
     public void close() {
-        mWriter.close();
+        if (mInitialized)
+            mWriter.close();
     }
 
     /**