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 d1f8edbbf..51a8e424f 100644
--- a/java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java
@@ -6,11 +6,9 @@ import org.broad.tribble.vcf.VCFHeaderLine;
 import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broad.tribble.vcf.VCFWriter;
 import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub;
 
 import java.io.*;
-import java.util.Set;
 
 import net.sf.samtools.util.BlockCompressedOutputStream;
 
@@ -68,8 +66,7 @@ public class VCFWriterStorage implements Storage<VCFWriterStorage>, VCFWriter {
             throw new StingException("Unable to open target output stream",ex);
         }
         writer = new StandardVCFWriter(this.stream);
-        Set<String> samples = SampleUtils.getSAMFileSamples(stub.getSAMFileHeader());
-        writer.writeHeader(new VCFHeader(null, samples));
+        writer.writeHeader(stub.getVCFHeader());
     }
 
     public void add(VariantContext vc, byte ref) {
@@ -109,7 +106,7 @@ public class VCFWriterStorage implements Storage<VCFWriterStorage>, VCFWriter {
 
             reader.close();
         } catch (IOException e) {
-            throw new StingException("Error reading file " + file + " in GATKVCFWriter: ", e);
+            throw new StingException("Error reading file " + file + " in VCFWriterStorage: ", e);
         }
     }    
 }
diff --git a/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java b/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java
index 5d5adda7c..237b3c734 100644
--- a/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java
@@ -98,7 +98,7 @@ public class VCFWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor {
 
     @Override
     public Object createTypeDefault(ArgumentSource source,Class type) {
-        VCFWriterStub stub = new VCFWriterStub(engine, defaultOutputStream, false);
+        VCFWriterStub stub = new VCFWriterStub(defaultOutputStream, false);
         engine.addOutput(stub);
         return stub;
     }
@@ -120,7 +120,7 @@ public class VCFWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor {
         boolean compress = writerFileName != null && SUPPORTED_ZIPPED_SUFFIXES.contains(getFileSuffix(writerFileName));
 
         // Create a stub for the given object.
-        VCFWriterStub stub = (writerFile != null) ? new VCFWriterStub(engine, writerFile, compress) : new VCFWriterStub(engine, System.out, compress);
+        VCFWriterStub stub = (writerFile != null) ? new VCFWriterStub(writerFile, compress) : new VCFWriterStub(System.out, compress);
 
         // WARNING: Side effects required by engine!
         parsingEngine.addTags(stub,getArgumentTags(matches));
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 1842e3d40..7cc4a77e8 100755
--- a/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterStub.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterStub.java
@@ -33,8 +33,6 @@ import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broad.tribble.vcf.VCFHeader;
 import org.broad.tribble.vcf.VCFWriter;
 import org.broadinstitute.sting.gatk.io.OutputTracker;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import net.sf.samtools.SAMFileHeader;
 
 /**
  * A stub for routing and management of genotype reading and writing.
@@ -44,11 +42,6 @@ import net.sf.samtools.SAMFileHeader;
  */
 public class VCFWriterStub implements Stub<VCFWriter>, VCFWriter {
 
-    /**
-     * Engine to use for collecting attributes for the output SAM file.
-     */
-    private final GenomeAnalysisEngine engine;
-
     /**
      * The file that this stub should write to.  Should be mutually
      * exclusive with genotypeStream.
@@ -61,6 +54,11 @@ public class VCFWriterStub implements Stub<VCFWriter>, VCFWriter {
      */
     private final PrintStream genotypeStream;
 
+    /**
+     * The cached VCF header (initilized to null)
+     */
+    private VCFHeader vcfHeader = null;
+
     /**
      * Should we emit a compressed output stream?
      */
@@ -74,12 +72,10 @@ public class VCFWriterStub implements Stub<VCFWriter>, VCFWriter {
 
     /**
      * Create a new stub given the requested file.
-     * @param engine        GATK engine.
      * @param genotypeFile  file to (ultimately) create.
      * @param isCompressed  should we compress the output stream?
      */
-    public VCFWriterStub(GenomeAnalysisEngine engine, File genotypeFile, boolean isCompressed) {
-        this.engine = engine;
+    public VCFWriterStub(File genotypeFile, boolean isCompressed) {
         this.genotypeFile = genotypeFile;
         this.genotypeStream = null;
         this.isCompressed = isCompressed;
@@ -87,12 +83,10 @@ public class VCFWriterStub implements Stub<VCFWriter>, VCFWriter {
 
     /**
      * Create a new stub given the requested file.
-     * @param engine        GATK engine.
      * @param genotypeStream  stream to (ultimately) write.
      * @param isCompressed  should we compress the output stream?
      */
-    public VCFWriterStub(GenomeAnalysisEngine engine, OutputStream genotypeStream, boolean isCompressed) {
-        this.engine = engine;
+    public VCFWriterStub(OutputStream genotypeStream, boolean isCompressed) {
         this.genotypeFile = null;
         this.genotypeStream = new PrintStream(genotypeStream);
         this.isCompressed = isCompressed;
@@ -126,8 +120,8 @@ public class VCFWriterStub implements Stub<VCFWriter>, VCFWriter {
      * Retrieves the header to use when creating the new file.
      * @return header to use when creating the new file.
      */
-    public SAMFileHeader getSAMFileHeader() {
-        return engine.getSAMFileHeader();
+    public VCFHeader getVCFHeader() {
+        return vcfHeader;
     }
 
     /**
@@ -139,6 +133,7 @@ public class VCFWriterStub implements Stub<VCFWriter>, VCFWriter {
     }
 
     public void writeHeader(VCFHeader header) {
+        vcfHeader = header;
         outputTracker.getStorage(this).writeHeader(header);
     }