diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyVariantCuts.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyVariantCuts.java
index b43fc5eeb..9dcd6d9ba 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyVariantCuts.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyVariantCuts.java
@@ -163,7 +163,7 @@ public class ApplyVariantCuts extends RodWalker<Integer, Integer> {
         final Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
         hInfo.addAll(VCFUtils.getHeaderFields(getToolkit()));
         hInfo.add(new VCFInfoHeaderLine("OQ", 1, VCFHeaderLineType.Float, "The original variant quality score"));
-        hInfo.add(new VCFHeaderLine("source", "VariantOptimizer"));
+        hInfo.add(new VCFHeaderLine("source", "ApplyVariantCuts"));
         final TreeSet<String> samples = new TreeSet<String>();
         samples.addAll(SampleUtils.getSampleListWithVCFHeader(getToolkit(), null));
         
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
index c8ce7604b..559431c8c 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
@@ -146,17 +146,6 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
                 throw new StingException( "Variant Optimization Model is unrecognized. Implemented options are GAUSSIAN_MIXTURE_MODEL and K_NEAREST_NEIGHBORS" );
         }
 
-        // setup the header fields
-        final Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
-        final TreeSet<String> samples = new TreeSet<String>();
-        hInfo.addAll(VCFUtils.getHeaderFields(getToolkit()));
-        hInfo.add(new VCFInfoHeaderLine("OQ", 1, VCFHeaderLineType.Float, "The original variant quality score"));
-        hInfo.add(new VCFHeaderLine("source", "VariantOptimizer"));
-        samples.addAll(SampleUtils.getUniqueSamplesFromRods(getToolkit()));
-
-        final VCFHeader vcfHeader = new VCFHeader(hInfo, samples);
-        vcfWriter.writeHeader(vcfHeader);
-
         boolean foundDBSNP = false;
         for( ReferenceOrderedDataSource d : this.getToolkit().getRodDataSources() ) {
             if( d.getName().startsWith("input") ) {
@@ -180,6 +169,18 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
             throw new StingException("dbSNP track is required. This calculation is critically dependent on being able to distinguish known and novel sites.");
         }
 
+        // setup the header fields
+        final Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
+        final TreeSet<String> samples = new TreeSet<String>();
+        hInfo.addAll(VCFUtils.getHeaderFields(getToolkit(), inputNames));
+        hInfo.add(new VCFInfoHeaderLine("OQ", 1, VCFHeaderLineType.Float, "The original variant quality score"));
+        hInfo.add(new VCFHeaderLine("source", "VariantRecalibrator"));
+        samples.addAll(SampleUtils.getUniqueSamplesFromRods(getToolkit()));
+
+        final VCFHeader vcfHeader = new VCFHeader(hInfo, samples);
+        vcfWriter.writeHeader(vcfHeader);
+
+
         // Set up default values for the FDR tranches if necessary
         if( FDR_TRANCHES == null ) {
             FDR_TRANCHES = new Double[5];
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
index 426343551..8e81afaba 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
@@ -43,9 +43,9 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
     public void testVariantRecalibrator() {
         HashMap<String, List<String>> e = new HashMap<String, List<String>>();
         e.put( validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf",
-                Arrays.asList("ad0868adddb2e837b4fc08f140e4d9c3", "937080353c7e03e11f8a70fc0004bf76","5b89fa5a4edf0080d64230d4103d2b8d")); // Each test checks the md5 of three output files
+                Arrays.asList("9c25a88c9fa48d7373029d2bfb40ad54", "937080353c7e03e11f8a70fc0004bf76","5b89fa5a4edf0080d64230d4103d2b8d")); // Each test checks the md5 of three output files
         e.put( validationDataLocation + "lowpass.N3.chr1.raw.0.vcf",
-                Arrays.asList("054d3228acfd6b02d24bfcf2fbd280a0", "f7c5c6cff9dd5280b25e24e0591e4cb0","1de1473db5720b882edf1381fa3dd039")); // Each test checks the md5 of three output files
+                Arrays.asList("074462f829ff553584e9b5e330be6d4b", "f7c5c6cff9dd5280b25e24e0591e4cb0","1de1473db5720b882edf1381fa3dd039")); // Each test checks the md5 of three output files
 
         for ( Map.Entry<String, List<String>> entry : e.entrySet() ) {
             String vcf = entry.getKey();
@@ -81,8 +81,8 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
     @Test
     public void testApplyVariantCuts() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "841deca1cb30a5a081cfbaa6f663e22a" );
-        e.put( validationDataLocation + "lowpass.N3.chr1.raw.0.vcf", "6234259e75fd7c1db31566dde1c55a82" );
+        e.put( validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "5b00a80b2a8fd078d6c2aa16924920e4" );
+        e.put( validationDataLocation + "lowpass.N3.chr1.raw.0.vcf", "d785380792da88f8d64fe1cf1133eeb0" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String vcf = entry.getKey();