diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
index 671e9e4e3..0227ac1ad 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
@@ -39,6 +39,7 @@ import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.CommandLineUtils;
 import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.vcf.VCFUtils;
 
 import java.util.*;
@@ -76,6 +77,7 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
     List<VariantContextUtils.JexlVCMatchExp> filterExps;
     List<VariantContextUtils.JexlVCMatchExp> genotypeFilterExps;
 
+    public static final String INPUT_VARIANT_ROD_BINDING_NAME = "variant";
     public static final String CLUSTERED_SNP_FILTER_NAME = "SnpCluster";
     private ClusteredSnps clusteredSNPs = null;
 
@@ -83,12 +85,15 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
     private FiltrationContextWindow variantContextWindow;
     private static final int windowSize = 10;  // 10 variants on either end of the current one
     private ArrayList<FiltrationContext> windowInitializer = new ArrayList<FiltrationContext>();
-    private boolean wroteHeader = false;
 
-    private void initializeVcfWriter(VariantContext vc) {
+    private void initializeVcfWriter() {
+
+        final ArrayList<String> inputNames = new ArrayList<String>();
+        inputNames.add( INPUT_VARIANT_ROD_BINDING_NAME );
+
         // setup the header fields
         Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
-        hInfo.addAll(VCFUtils.getHeaderFields(getToolkit()));
+        hInfo.addAll(VCFUtils.getHeaderFields(getToolkit(), inputNames));
 
         if ( clusterWindow > 0 )
             hInfo.add(new VCFFilterHeaderLine(CLUSTERED_SNP_FILTER_NAME, "SNPs found in clusters"));
@@ -109,7 +114,7 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
             }
         }
 
-        writer.writeHeader(new VCFHeader(hInfo, vc.getSampleNames()));
+        writer.writeHeader(new VCFHeader(hInfo, SampleUtils.getUniqueSamplesFromRods(getToolkit(), inputNames)));
     }
 
     public void initialize() {
@@ -120,6 +125,8 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
         genotypeFilterExps = VariantContextUtils.initializeMatchExps(GENOTYPE_FILTER_NAMES, GENOTYPE_FILTER_EXPS);
 
         VariantContextUtils.engine.setSilent(true);
+
+        initializeVcfWriter();
     }
 
     public Integer reduceInit() { return 0; }
@@ -136,12 +143,12 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
         if ( tracker == null )
             return 0;
 
-        List<Object> rods = tracker.getReferenceMetaData("variant");
+        List<Object> rods = tracker.getReferenceMetaData( INPUT_VARIANT_ROD_BINDING_NAME );
         // ignore places where we don't have a variant
         if ( rods.size() == 0 )
             return 0;
 
-        VariantContext vc = VariantContextAdaptors.toVariantContext("variant", rods.get(0), ref);
+        VariantContext vc = VariantContextAdaptors.toVariantContext( INPUT_VARIANT_ROD_BINDING_NAME, rods.get(0), ref );
         FiltrationContext varContext = new FiltrationContext(tracker, ref, vc);
 
         // if we're still initializing the context, do so
@@ -216,15 +223,7 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
         else
             filteredVC = new VariantContext(vc.getName(), vc.getChr(), vc.getStart(), vc.getEnd(), vc.getAlleles(), genotypes, vc.getNegLog10PError(), filters, vc.getAttributes());
 
-        writeVCF(filteredVC, context.getReferenceContext().getBase());
-    }
-
-    private void writeVCF(VariantContext vc, byte ref) {
-        if ( !wroteHeader ) {
-            initializeVcfWriter(vc);
-            wroteHeader = true;
-        }
-        writer.add(vc, ref);
+        writer.add( filteredVC, context.getReferenceContext().getBase() );
     }
 
     public Integer reduce(Integer value, Integer sum) {
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java
index 8478fdf11..4d722f5ea 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java
@@ -16,7 +16,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testNoAction() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("a08a88866aac0ec4a844386bea5c585f"));
+                Arrays.asList("1faa4662400a1128b94d5f93d46eee1d"));
         executeTest("test no action", spec);
     }
 
@@ -24,7 +24,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testClusteredSnps() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -window 10 -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("59f0f365550cc01e0fdef65e98963826"));
+                Arrays.asList("f09454e99562d839e5117f992f4eebef"));
         executeTest("test clustered SNPs", spec);
     }
 
@@ -32,7 +32,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testMask() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -mask foo -B:mask,VCF " + validationDataLocation + "vcfexample2.vcf -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("cb67d20027e4e0cb45544a69ff49476e"));
+                Arrays.asList("4b1d370e60c2bc0c763886c3adff473a"));
         executeTest("test mask", spec);
     }
 
@@ -40,7 +40,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testFilter1() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -filter 'DoC < 20 || FisherStrand > 20.0' -filterName foo -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("1fdccdb8ca837d5fc7a619d285e2308a"));
+                Arrays.asList("3ea5495c6eace03971cb4c6cd1f84af4"));
         executeTest("test filter #1", spec);
     }
 
@@ -48,7 +48,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testFilter2() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -filter 'AlleleBalance < 70.0 && FisherStrand == 1.4' -filterName bar -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("40fdd0321091402a669d7e2eaadf072a"));
+                Arrays.asList("b45f3ac20397ab4b64c963ce67cf9cca"));
         executeTest("test filter #2", spec);
     }
 
@@ -56,7 +56,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testFilterWithSeparateNames() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --filterName ABF -filter 'AlleleBalance < 0.7' --filterName FSF -filter 'FisherStrand == 1.4' -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("a017fbbb6d610481b174c53d29b1ae5a"));
+                Arrays.asList("d2484ea8f1d1b12b5586e9bab518d7fa"));
         executeTest("test filter with separate names #2", spec);
     }
 
@@ -64,7 +64,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testGenotypeFilter1() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -G_filter 'GQ == 0.60' -G_filterName foo -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("1a200b0e47cac16d1dfd8ce44484c667"));
+                Arrays.asList("76a37ff57ae5c93f5abf341203f7af2c"));
         executeTest("test genotype filter #1", spec);
     }
 
@@ -72,7 +72,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testGenotypeFilter2() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -G_filter 'AF == 0.04 && isHomVar == 1' -G_filterName foo -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("78315a09eb3ac8cc47010bb92fad342f"));
+                Arrays.asList("e8b80ce01f631c840336792cfbf35254"));
         executeTest("test genotype filter #2", spec);
     }
 }
\ No newline at end of file