diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java
index 6b887aa15..bd3f0bb76 100644
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java
@@ -62,8 +62,6 @@ class BCF2Writer extends IndexingVariantContextWriter {
 
     @Override
     public void writeHeader(final VCFHeader header) {
-        this.header = header;
-
         // create the config offsets map
         for ( final VCFContigHeaderLine contig : header.getContigLines())
             contigDictionary.put(contig.getID(), contig.getContigIndex());
@@ -78,7 +76,7 @@ class BCF2Writer extends IndexingVariantContextWriter {
             // write out the header into a byte stream, get it's length, and write everything to the file
             final ByteArrayOutputStream capture = new ByteArrayOutputStream();
             final OutputStreamWriter writer = new OutputStreamWriter(capture);
-            VCFWriter.writeHeader(header, writer, doNotWriteGenotypes, VCFWriter.getVersionLine(), "BCF2 stream");
+            this.header = VCFWriter.writeHeader(header, writer, doNotWriteGenotypes, VCFWriter.getVersionLine(), "BCF2 stream");
             writer.append('\0'); // the header is null terminated by a byte
             writer.close();
 
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 24f1921a8..d080d1754 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
@@ -90,8 +90,9 @@ class VCFWriter extends IndexingVariantContextWriter {
 
     @Override
     public void writeHeader(VCFHeader header) {
-        mHeader = header;
-        writeHeader(mHeader, mWriter, doNotWriteGenotypes, getVersionLine(), getStreamName());
+        // note we need to update the mHeader object after this call because they header
+        // may have genotypes trimmed out of it, if doNotWriteGenotypes is true
+        mHeader = writeHeader(header, mWriter, doNotWriteGenotypes, getVersionLine(), getStreamName());
 
         // determine if we use filters, so we should FORCE pass the records
         // TODO -- this might not be necessary any longer as we have unfiltered, filtered, and PASS VCs
@@ -105,11 +106,11 @@ class VCFWriter extends IndexingVariantContextWriter {
         return VERSION_LINE;
     }
 
-    public static void writeHeader(VCFHeader header,
-                                   final Writer writer,
-                                   final boolean doNotWriteGenotypes,
-                                   final String versionLine,
-                                   final String streamNameForError) {
+    public static VCFHeader writeHeader(VCFHeader header,
+                                        final Writer writer,
+                                        final boolean doNotWriteGenotypes,
+                                        final String versionLine,
+                                        final String streamNameForError) {
         header = doNotWriteGenotypes ? new VCFHeader(header.getMetaData()) : header;
         
         try {
@@ -151,6 +152,8 @@ class VCFWriter extends IndexingVariantContextWriter {
         catch (IOException e) {
             throw new ReviewedStingException("IOException writing the VCF header to " + streamNameForError, e);
         }
+
+        return header;
     }
 
     /**