diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFs.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFs.java
index ac9b8c4fa..093bb061b 100644
--- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFs.java
+++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFs.java
@@ -154,8 +154,12 @@ public class GenotypeGVCFs extends RodWalker<VariantContext, VariantContextWrite
         // create the annotation engine
         annotationEngine = new VariantAnnotatorEngine(Arrays.asList("none"), annotationsToUse, Collections.<String>emptyList(), this, getToolkit());
 
+        // collect the actual rod bindings into a list for use later
+        for ( final RodBindingCollection<VariantContext> variantCollection : variantCollections )
+            variants.addAll(variantCollection.getRodBindings());
+
         // take care of the VCF headers
-        final Map<String, VCFHeader> vcfRods = GATKVCFUtils.getVCFHeadersFromRods(getToolkit());
+        final Map<String, VCFHeader> vcfRods = GATKVCFUtils.getVCFHeadersFromRods(getToolkit(), variants);
         final Set<VCFHeaderLine> headerLines = VCFUtils.smartMergeHeaders(vcfRods.values(), true);
         headerLines.addAll(annotationEngine.getVCFAnnotationDescriptions());
         VCFStandardHeaderLines.addStandardInfoLines(headerLines, true, VCFConstants.MLE_ALLELE_COUNT_KEY, VCFConstants.MLE_ALLELE_FREQUENCY_KEY);
@@ -167,11 +171,7 @@ public class GenotypeGVCFs extends RodWalker<VariantContext, VariantContextWrite
         vcfWriter.writeHeader(vcfHeader);
 
         // create the genotyping engine
-        genotypingEngine = new UnifiedGenotypingEngine(getToolkit(), new UnifiedArgumentCollection(),samples);
-
-        // collect the actual rod bindings into a list for use later
-        for ( final RodBindingCollection<VariantContext> variantCollection : variantCollections )
-            variants.addAll(variantCollection.getRodBindings());
+        genotypingEngine = new UnifiedGenotypingEngine(getToolkit(), new UnifiedArgumentCollection(), samples);
     }
 
     public VariantContext map(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context) {
diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFsIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
index 547d3ef3e..4af465c69 100644
--- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
+++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
@@ -102,7 +102,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
                         " -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
                         " -L 20:10,000,000-11,000,000 --dbsnp " + b37dbSNP132, b37KGReference),
                 1,
-                Arrays.asList("91061171c480901df8f776090527c182"));
+                Arrays.asList("dc13542c71fbb4846507b0cdcc4827be"));
         executeTest("combineSingleSamplePipelineGVCF_addDbsnp", spec);
     }