diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
index f2b2dfb7d..c768f95ad 100755
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
@@ -96,7 +96,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     //
     // --------------------------------------------------------------------------------------------------------------
 
-    private final static String COMPRESSED_OUTPUT_MD5 = "5b8f477c287770b5769b05591e35bc2d";
+    private final static String COMPRESSED_OUTPUT_MD5 = "3eba6c309514d1e9ee06a20a112b68e6";
 
     @Test
     public void testCompressedOutput() {
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriter.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriter.java
index 9a987f161..974e50ced 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriter.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriter.java
@@ -248,7 +248,8 @@ class VCFWriter extends IndexingVariantContextWriter {
             }
             
             mWriter.write("\n");
-            mWriter.flush();  // necessary so that writing to an output stream will work
+            // note that we cannot call flush here if we want block gzipping to work properly
+            // calling flush results in all gzipped blocks for each variant
         } catch (IOException e) {
             throw new RuntimeException("Unable to write the VCF object to " + getStreamName(), e);
         }