diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/concordance/IndelSubsets.java b/java/src/org/broadinstitute/sting/gatk/walkers/concordance/IndelSubsets.java
index c3ee233d7..041256c29 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/concordance/IndelSubsets.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/concordance/IndelSubsets.java
@@ -66,7 +66,7 @@ public class IndelSubsets implements ConcordanceType {
             return null;
 
         // only deal with a valid indel
-        Variation indel = ( indel1 != null ? indel1.toVariation() : indel2.toVariation() );
+        Variation indel = ( indel1 != null ? indel1.toVariation(ref.getBase()) : indel2.toVariation(ref.getBase()) );
 
         // we only deal with the first allele
         int size = ( indel.getAlternateAlleleList().get(0).length() <= sizeCutoff ? 0 : 1 );
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/concordance/SimpleVenn.java b/java/src/org/broadinstitute/sting/gatk/walkers/concordance/SimpleVenn.java
index 43e22840c..3a4a97bea 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/concordance/SimpleVenn.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/concordance/SimpleVenn.java
@@ -42,8 +42,8 @@ public class SimpleVenn implements ConcordanceType {
             return sample2 + "_only";
 
         // at this point we know that neither is null, so now we need to test for alternate allele concordance
-        Variation callV1 = call1.toVariation();
-        Variation callV2 = call2.toVariation();
+        Variation callV1 = call1.toVariation(ref.getBase());
+        Variation callV2 = call2.toVariation(ref.getBase());
 
         // we can't really deal with multi-allelic variants
         if ( callV1.isBiallelic() && callV2.isBiallelic() ) {
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/BasicGenotype.java b/java/src/org/broadinstitute/sting/utils/genotype/BasicGenotype.java
index 2082d127a..94a44d9d7 100644
--- a/java/src/org/broadinstitute/sting/utils/genotype/BasicGenotype.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/BasicGenotype.java
@@ -151,9 +151,9 @@ public class BasicGenotype implements Genotype {
      * @return the variant
      */
     @Override
-    public Variation toVariation() {
-        if (!isVariant(this.mRef)) throw new IllegalStateException("this genotype is not a variant");
-        return new BasicVariation(this.getBases(), String.valueOf(mRef), this.getBases().length(), mLocation, mNegLog10PError);
+    public Variation toVariation(char ref) {
+        if (!isVariant(ref)) throw new IllegalStateException("this genotype is not a variant");
+        return new BasicVariation(this.getBases(), String.valueOf(ref), this.getBases().length(), mLocation, mNegLog10PError);
     }
 
     /**
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/Genotype.java b/java/src/org/broadinstitute/sting/utils/genotype/Genotype.java
index cc0ad15be..1adf93399 100644
--- a/java/src/org/broadinstitute/sting/utils/genotype/Genotype.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/Genotype.java
@@ -77,8 +77,9 @@ public interface Genotype {
     /**
      * return this genotype as a variant
      *
+     * @param ref the reference base
      * @return the variant
      */
-    public Variation toVariation();
+    public Variation toVariation(char ref);
 
 }
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/geli/GeliGenotypeCall.java b/java/src/org/broadinstitute/sting/utils/genotype/geli/GeliGenotypeCall.java
index 150fdf4e7..b23cf7901 100755
--- a/java/src/org/broadinstitute/sting/utils/genotype/geli/GeliGenotypeCall.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/geli/GeliGenotypeCall.java
@@ -201,7 +201,7 @@ public class GeliGenotypeCall implements Genotype, ReadBacked, PosteriorsBacked
      * @return true if we're a variant
      */
     public boolean isVariant(char ref) {
-        return !Utils.dupString(this.getReference(), 2).equals(getBestGenotype().toString());
+        return !Utils.dupString(ref, 2).equals(getBestGenotype().toString());
     }
 
     /**
@@ -217,9 +217,9 @@ public class GeliGenotypeCall implements Genotype, ReadBacked, PosteriorsBacked
      *
      * @return return this genotype as a variant
      */
-    public Variation toVariation() {
+    public Variation toVariation(char ref) {
         double bestRef = Math.abs(mPosteriors[getBestGenotype().ordinal()] - mPosteriors[getRefGenotype().ordinal()]);
-        return new BasicVariation(this.getBases(), String.valueOf(this.getReference()), 0, this.mLocation, bestRef);
+        return new BasicVariation(this.getBases(), String.valueOf(ref), 0, this.mLocation, bestRef);
     }
 
     /**
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFGenotypeCall.java b/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFGenotypeCall.java
index 8186d5a28..999e58a05 100755
--- a/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFGenotypeCall.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFGenotypeCall.java
@@ -120,7 +120,7 @@ public class GLFGenotypeCall implements Genotype, ReadBacked, LikelihoodsBacked
      *
      * @return return this genotype as a variant
      */
-    public Variation toVariation() {
+    public Variation toVariation(char ref) {
         throw new UnsupportedOperationException("GLF call doesn't support conversion to Variation");
     }
 
@@ -154,15 +154,6 @@ public class GLFGenotypeCall implements Genotype, ReadBacked, LikelihoodsBacked
         return !Utils.dupString(mRefBase, 2).equals(mGenotype);
     }
 
-    /**
-     * are we a variant? (non-ref)
-     *
-     * @return true if we're a variant
-     */
-    public boolean isVariant() {
-        return isVariant(mRefBase);
-    }
-
     /**
      * get the SAM records that back this genotype call
      *
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeCall.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeCall.java
index 6473e2cd5..c36a217ac 100755
--- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeCall.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeCall.java
@@ -207,7 +207,7 @@ public class VCFGenotypeCall implements Genotype, ReadBacked, PosteriorsBacked,
      * @return true if we're a variant
      */
     public boolean isVariant(char ref) {
-        return !Utils.dupString(this.getReference(), 2).equals(getBestGenotype().toString());
+        return !Utils.dupString(ref, 2).equals(getBestGenotype().toString());
     }
 
     /**
@@ -223,9 +223,9 @@ public class VCFGenotypeCall implements Genotype, ReadBacked, PosteriorsBacked,
      *
      * @return return this genotype as a variant
      */
-    public Variation toVariation() {
+    public Variation toVariation(char ref) {
         double bestRef = Math.abs(mPosteriors[getBestGenotype().ordinal()] - mPosteriors[getRefGenotype().ordinal()]);
-        return new BasicVariation(this.getBases(), String.valueOf(this.getReference()), 0, this.mLocation, bestRef);
+        return new BasicVariation(this.getBases(), String.valueOf(ref), 0, this.mLocation, bestRef);
     }
 
     /**