diff --git a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
index 4a20e2951..4ab7d466d 100755
--- a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
+++ b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
@@ -171,8 +171,8 @@ public class VariantContextUtils {
         UNION, INTERSECT
     }
 
-    public static VariantContext simpleMerge(Collection<VariantContext> unsortedVCs, byte[] refBases) {
-        return simpleMerge(unsortedVCs, null, VariantMergeType.INTERSECT, GenotypeMergeType.UNSORTED, false, false, refBases);
+    public static VariantContext simpleMerge(Collection<VariantContext> unsortedVCs, byte refBase) {
+        return simpleMerge(unsortedVCs, null, VariantMergeType.INTERSECT, GenotypeMergeType.UNSORTED, false, false, refBase);
     }
 
 
@@ -189,14 +189,14 @@ public class VariantContextUtils {
      */
     public static VariantContext simpleMerge(Collection<VariantContext> unsortedVCs, List<String> priorityListOfVCs,
                                              VariantMergeType variantMergeOptions, GenotypeMergeType genotypeMergeOptions,
-                                             boolean annotateOrigin, boolean printMessages, byte[] inputRefBases ) {
+                                             boolean annotateOrigin, boolean printMessages, byte inputRefBase ) {
 
-        return simpleMerge(unsortedVCs, priorityListOfVCs, variantMergeOptions, genotypeMergeOptions, annotateOrigin, printMessages, inputRefBases, "set");
+        return simpleMerge(unsortedVCs, priorityListOfVCs, variantMergeOptions, genotypeMergeOptions, annotateOrigin, printMessages, inputRefBase, "set");
     }
 
 public static VariantContext simpleMerge(Collection<VariantContext> unsortedVCs, List<String> priorityListOfVCs,
                                          VariantMergeType variantMergeOptions, GenotypeMergeType genotypeMergeOptions,
-                                         boolean annotateOrigin, boolean printMessages, byte[] inputRefBases, String setKey ) {
+                                         boolean annotateOrigin, boolean printMessages, byte inputRefBase, String setKey ) {
         if ( unsortedVCs == null || unsortedVCs.size() == 0 )
             return null;
 
@@ -213,7 +213,7 @@ public static VariantContext simpleMerge(Collection<VariantContext> unsortedVCs,
         List<VariantContext> VCs = new ArrayList<VariantContext>();
 
         for (VariantContext vc : prepaddedVCs) {
-            VCs.add(createVariantContextWithPaddedAlleles(vc,inputRefBases));
+            VCs.add(createVariantContextWithPaddedAlleles(vc,inputRefBase));
         }
 
 
@@ -479,7 +479,7 @@ public static VariantContext simpleMerge(Collection<VariantContext> unsortedVCs,
 
     }
 
-    public static VariantContext createVariantContextWithPaddedAlleles(VariantContext inputVC, byte[] inputRefBase) {
+    public static VariantContext createVariantContextWithPaddedAlleles(VariantContext inputVC, byte inputRefBase) {
         Allele refAllele = inputVC.getReference();
 
 
@@ -501,8 +501,8 @@ public static VariantContext simpleMerge(Collection<VariantContext> unsortedVCs,
 
             Map<String,Object> attributes = inputVC.getAttributes();
 
-            if (BaseUtils.isRegularBase(inputRefBase[0]))
-                refByte = inputRefBase[0];
+            if (BaseUtils.isRegularBase(inputRefBase))
+                refByte = inputRefBase;
             else if (attributes.containsKey(VariantContext.REFERENCE_BASE_FOR_INDEL_KEY))
                 refByte = (Byte)attributes.get(VariantContext.REFERENCE_BASE_FOR_INDEL_KEY);
             else
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java b/java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java
index 8c7b8279f..7d34eeae7 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java
@@ -129,7 +129,7 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
         }
 
         vc = VariantContextUtils.purgeUnallowedGenotypeAttributes(vc, allowedGenotypeFormatStrings);
-        vcfwriter.add(vc, new byte[]{ref});
+        vcfwriter.add(vc,ref);
     }
 
     public Integer reduceInit() {
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
index aca29d7e7..ca696e664 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
@@ -202,12 +202,12 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
 
         if ( ! indelsOnly ) {
             for ( VariantContext annotatedVC : annotatedVCs )
-                vcfWriter.add(annotatedVC, new byte[]{ref.getBase()});
+                vcfWriter.add(annotatedVC, ref.getBase());
         } else {
             // check to see if the buffered context is different (in location) this context
             if ( indelBufferContext != null && ! indelBufferContext.iterator().next().getLocation().equals(annotatedVCs.iterator().next().getLocation()) ) {
                 for ( VariantContext annotatedVC : indelBufferContext )
-                    vcfWriter.add(annotatedVC, new byte[]{ref.getBase()});
+                    vcfWriter.add(annotatedVC, ref.getBase());
                 indelBufferContext = annotatedVCs;
             } else {
                 indelBufferContext = annotatedVCs;
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 cc36e44c3..6a6678ee7 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
@@ -216,7 +216,7 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
     private void writeVCF(VariantContext vc, byte ref) {
         if ( writer == null )
             initializeVcfWriter(vc);
-        writer.add(vc, new byte[]{ref});
+        writer.add(vc, ref);
     }
 
     public Integer reduce(Integer value, Integer sum) {
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BatchedCallsMerger.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BatchedCallsMerger.java
index a72ed4552..3f65c0677 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BatchedCallsMerger.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BatchedCallsMerger.java
@@ -148,7 +148,7 @@ public class BatchedCallsMerger extends LocusWalker<VariantContext, Integer> imp
         }
 
         // merge the variant contexts
-        return VariantContextUtils.simpleMerge(calls, ref.getBases());
+        return VariantContextUtils.simpleMerge(calls, ref.getBase());
     }
 
     private AlignmentContext filterForSamples(ReadBackedPileup pileup, Set<String> samples) {
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java b/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java
index e075a695c..db0759b4b 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java
@@ -160,7 +160,7 @@ public class SequenomValidationConverter extends RodWalker<Pair<VariantContext,
         vcfWriter.writeHeader(header);
 
         for ( Pair<VariantContext, Byte> record : records )
-            vcfWriter.add(record.first, new byte[]{record.second});
+            vcfWriter.add(record.first, record.second);
         vcfWriter.close();
     }
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
index 83732cfb6..4b69e4be2 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
@@ -554,7 +554,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
                 wroteHeader = true;
             }
 
-            writer.add(mvc, new byte[]{ref});
+            writer.add(mvc, ref);
             //interestingReasons.clear();
         }
     }
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 52035108d..b8a875777 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyVariantCuts.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyVariantCuts.java
@@ -150,7 +150,7 @@ public class ApplyVariantCuts extends RodWalker<Integer, Integer> {
                         vc = new VariantContext(vc.getName(), vc.getLocation(), vc.getAlleles(), vc.getGenotypes(), vc.getNegLog10PError(), filters, vc.getAttributes());
                     }
                 }
-                vcfWriter.add( vc, new byte[]{ref.getBase()} );
+                vcfWriter.add( vc, ref.getBase() );
             }
 
         }
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 d3c3e6b60..eb72f6db7 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
@@ -194,10 +194,10 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
                     filters.add(VCFConstants.PASSES_FILTERS_v4);
                     VariantContext newVC = new VariantContext(vc.getName(), vc.getLocation(), vc.getAlleles(), vc.getGenotypes(), variantDatum.qual / 10.0, filters, attrs);
 
-                    vcfWriter.add( newVC, new byte[]{ref.getBase()} );
+                    vcfWriter.add( newVC, ref.getBase() );
 
                 } else { // not a SNP or is filtered so just dump it out to the VCF file
-                    vcfWriter.add( vc, new byte[]{ref.getBase()} ); 
+                    vcfWriter.add( vc, ref.getBase() ); 
                 }
             }
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
index 8f1510d43..9157131e9 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
@@ -116,14 +116,14 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
         // Need to provide reference bases to simpleMerge starting at current locus
         Collection<VariantContext> vcs = tracker.getAllVariantContexts(ref, context.getLocation());
         VariantContext mergedVC = VariantContextUtils.simpleMerge(vcs, priority, variantMergeOption,
-                genotypeMergeOption, true, printComplexMerges, ref.getBasesAtLocus(1), SET_KEY);
+                genotypeMergeOption, true, printComplexMerges, ref.getBase(), SET_KEY);
 
 
         //out.printf("   merged => %s%nannotated => %s%n", mergedVC, annotatedMergedVC);
 
         if ( mergedVC != null ) { // only operate at the start of events
             VariantContext annotatedMergedVC = engine.annotateContext(tracker, ref, mergedVC);
-            vcfWriter.add(annotatedMergedVC, ref.getBasesAtLocus(1));
+            vcfWriter.add(annotatedMergedVC, ref.getBase());
         }
 
         return vcs.isEmpty() ? 0 : 1;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
index 5a6d2c231..be8f62654 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
@@ -64,7 +64,7 @@ public class FilterLiftedVariants extends RodWalker<Integer, Integer> {
         if ( recordRef != ref ) {
             failedLocs++;
         } else {
-            writer.add(vc, new byte[]{ref});
+            writer.add(vc, ref);
         }
     }
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
index cf2828eea..4010d70bf 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
@@ -86,7 +86,7 @@ public class LiftoverVariants extends RodWalker<Integer, Integer> {
 
         if ( toInterval != null ) {
             vc = VariantContextUtils.modifyLocation(vc, GenomeLocParser.createGenomeLoc(toInterval.getSequence(), toInterval.getStart(), toInterval.getEnd()));
-            writer.add(vc, new byte[]{ref.getBase()});
+            writer.add(vc, ref.getBase());
             successfulIntervals++;
         } else {
             failedIntervals++;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelAnnotator.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelAnnotator.java
index b561cfdb0..eaa42b354 100644
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelAnnotator.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelAnnotator.java
@@ -109,7 +109,7 @@ public class IndelAnnotator extends RodWalker<Integer,Long>{
         Map<String, Object> attrs = new HashMap<String, Object>(vc.getAttributes());
         attrs.put("type",annotationString);
         vc = VariantContextUtils.modifyAttributes(vc, attrs);
-        vcfWriter.add(vc, new byte[]{ref.getBase()});
+        vcfWriter.add(vc, ref.getBase());
 
         return 1;
     }
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelDBRateWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelDBRateWalker.java
index 4a9b2d5b6..3acbf3538 100644
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelDBRateWalker.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelDBRateWalker.java
@@ -142,12 +142,12 @@ public class IndelDBRateWalker extends RodWalker<OverlapTable,OverlapTabulator>
         if ( vcfWriter != null ) {
             int i = 0;
             while ( i < compContexts.size() && compContexts.get(i).getLocation().isBefore(evalContexts.get(0).getLocation())) {
-                vcfWriter.add(compContexts.get(i), new byte[]{compContexts.get(i).getReference().getBases()[0]});
+                vcfWriter.add(compContexts.get(i),compContexts.get(i).getReference().getBases()[0]);
                 i++;
             }
-            vcfWriter.add(evalContexts.get(0), new byte[]{ref.getBase()});
+            vcfWriter.add(evalContexts.get(0), ref.getBase());
             while ( i < compContexts.size() && compContexts.get(i).getLocation().distance(evalContexts.get(0).getLocation()) <= indelWindow) {
-                vcfWriter.add(compContexts.get(i), new byte[]{compContexts.get(i).getReference().getBases()[0]});
+                vcfWriter.add(compContexts.get(i), compContexts.get(i).getReference().getBases()[0]);
                 i++;
             }
         }
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MendelianViolationClassifier.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MendelianViolationClassifier.java
index 097cd5847..9a699839f 100644
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MendelianViolationClassifier.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MendelianViolationClassifier.java
@@ -601,7 +601,7 @@ public class MendelianViolationClassifier extends LocusWalker<MendelianViolation
     public VCFWriter reduce(MendelianViolation variant, VCFWriter writer) {
         if ( variant != null ) {
             trioStructure.updateHomozygosityRegions(variant,bedOutput);
-            writer.add(variant.toVariantContext(), new byte[]{variant.getRefBase()});
+            writer.add(variant.toVariantContext(),variant.getRefBase());
         }
 
         return writer;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestVariantContextWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestVariantContextWalker.java
index c2253a49d..17c810f65 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestVariantContextWalker.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestVariantContextWalker.java
@@ -77,7 +77,7 @@ public class TestVariantContextWalker extends RodWalker<Integer, Integer> {
                         wroteHeader = true;
                     }
 
-                    writer.add(vc, new byte[]{ref.getBase()});
+                    writer.add(vc, ref.getBase());
                 }
 
                 n++;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/VCF4WriterTestWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/VCF4WriterTestWalker.java
index 5834309dc..46c5ff0cb 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/VCF4WriterTestWalker.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/VCF4WriterTestWalker.java
@@ -126,7 +126,7 @@ public class VCF4WriterTestWalker extends RodWalker<Integer, Integer> {
             return 0;
 
         // Write directly variant context to VCF4.0 format.
-        vcfWriter.add(vc, ref.getBases());
+        vcfWriter.add(vc, ref.getBase());
 
         return 1;
     }
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java
index 35f7e9940..1ecc313f0 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java
@@ -317,7 +317,7 @@ public class BeagleOutputToVCFWalker  extends RodWalker<Integer, Integer> {
 
 
 
-        vcfWriter.add(VariantContextUtils.modifyAttributes(filteredVC, attributes), new byte[]{ref.getBase()});
+        vcfWriter.add(VariantContextUtils.modifyAttributes(filteredVC, attributes), ref.getBase());
 
 
         return 1;
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/TrioGenotyperWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/TrioGenotyperWalker.java
index 6a0759ac8..59d514d5d 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/TrioGenotyperWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/TrioGenotyperWalker.java
@@ -179,7 +179,7 @@ public class TrioGenotyperWalker extends RefWalker<VariantContext, Integer>{
             if ( a == 0 )
                 writer.writeHeader(VariantContextAdaptors.createVCFHeader(null, vc));
 
-            writer.add(vc, new byte[]{(byte)'.'});
+            writer.add(vc, (byte)'.');
             a++;
         }
 
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotator.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotator.java
index 8e56133f0..07c57a585 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotator.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotator.java
@@ -303,7 +303,7 @@ public class GenomicAnnotator extends RodWalker<LinkedList<VariantContext>, Link
         } else {
             //write results to disk immediately
             for(VariantContext annotatedVC : annotatedVCs ) {
-                vcfWriter.add(annotatedVC, new byte[]{ref.getBase()});
+                vcfWriter.add(annotatedVC,ref.getBase());
             }
         }
 
@@ -346,7 +346,7 @@ public class GenomicAnnotator extends RodWalker<LinkedList<VariantContext>, Link
         if(multiThreadedMode) {
             //finally write results to disk
             for(VariantContext vc : totalOutputRecords ) {
-                vcfWriter.add(vc, vc.getReference().getBases());
+                vcfWriter.add(vc, vc.getReference().getBases()[0]);
             }
         }
 
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VariantSelect.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VariantSelect.java
index 2ddbeff48..e772e7208 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VariantSelect.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VariantSelect.java
@@ -139,7 +139,7 @@ public class VariantSelect extends RodWalker<Integer, Integer> {
         }
 
         if ( someoneMatched )
-            writer.add(vc, new byte[]{ref.getBase()});
+            writer.add(vc, ref.getBase());
 
         return 1;
     }
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VariantSubset.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VariantSubset.java
index edf4c0b0c..df901557f 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VariantSubset.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VariantSubset.java
@@ -73,7 +73,7 @@ public class VariantSubset extends RodWalker<Integer, Integer> {
 
             if ( (vc.isPolymorphic() || INCLUDE_NON_VARIANTS) &&
                     (!subset.isFiltered() || INCLUDE_FILTERED) )
-                writer.add(subset, new byte[]{ref.getBase()});
+                writer.add(subset, ref.getBase());
         }
 
         return 1;
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java
index 91008f7af..3dd6feffb 100644
--- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java
@@ -63,7 +63,7 @@ public class VCFGenotypeWriterAdapter extends VCFWriter implements VCFGenotypeWr
 
     public void addCall(VariantContext vc, byte ref) {
         vc = VariantContextUtils.purgeUnallowedGenotypeAttributes(vc, allowedGenotypeFormatKeys);
-        add(vc, new byte[]{ref});
+        add(vc, ref);
     }
 
     public void writeHeader(VCFHeader header) {
@@ -112,7 +112,7 @@ public class VCFGenotypeWriterAdapter extends VCFWriter implements VCFGenotypeWr
             while ( iterator.hasNext() ) {
                 VariantContext vc = iterator.next();
                 vc = VariantContextUtils.purgeUnallowedGenotypeAttributes(vc, allowedGenotypeFormatKeys);
-                add(vc, new byte[]{vc.getReferenceBaseForIndel()});
+                add(vc, vc.getReferenceBaseForIndel());
             }
             vcfReader.close();
         } catch (FileNotFoundException e) {
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFWriter.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFWriter.java
index 0aac8bc2f..ef354735b 100644
--- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFWriter.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFWriter.java
@@ -133,15 +133,13 @@ public class VCFWriter {
         }
     }
 
-    public void add(VariantContext vc, byte[] refBases) {
+    public void add(VariantContext vc, byte refBase) {
         if ( mHeader == null )
             throw new IllegalStateException("The VCF Header must be written before records can be added");
-        if ( refBases == null || refBases.length < 1 )
-            throw new IllegalArgumentException("The reference base must be provided to write VCF records");
 
         try {
 
-            vc = VariantContextUtils.createVariantContextWithPaddedAlleles(vc, refBases);
+            vc = VariantContextUtils.createVariantContextWithPaddedAlleles(vc, refBase);
 
             GenomeLoc loc = vc.getLocation();
             Map<Allele, String> alleleMap = new HashMap<Allele, String>(vc.getAlleles().size());
diff --git a/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java b/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java
index 1cbea1029..d209740b4 100644
--- a/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java
+++ b/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java
@@ -47,8 +47,8 @@ public class VCFWriterUnitTest extends BaseTest {
         VCFHeader header = createFakeHeader(metaData,additionalColumns);
         VCFWriter writer = new VCFWriter(fakeVCFFile);
         writer.writeHeader(header);
-        writer.add(createVC(header),"A".getBytes());
-        writer.add(createVC(header),"A".getBytes());
+        writer.add(createVC(header),new Byte("A"));
+        writer.add(createVC(header),new Byte("A"));
         writer.close();
         VCFCodec reader = new VCFCodec();
         AsciiLineReader lineReader;