diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java b/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
index 1505f029c..218cef8eb 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
@@ -239,12 +239,12 @@ public class VariantContextAdaptors {
 
     private static Allele determineRefAllele(VCFRecord vcf, ReferenceContext ref) {
         Allele refAllele;
-        if ( ref == null ) {
+        if ( vcf.isInsertion() ) {
+            refAllele = new Allele(Allele.NULL_ALLELE_STRING, true);
+        } else if ( ref == null ) {
             refAllele = new Allele(vcf.getReference(), true);
         } else if ( !vcf.isIndel() ) {
             refAllele = new Allele(Character.toString(ref.getBase()), true);
-        } else if ( vcf.isInsertion() ) {
-            refAllele = new Allele(Allele.NULL_ALLELE_STRING, true);
         } else if ( vcf.isDeletion() ) {
             int start = (int)(ref.getLocus().getStart() - ref.getWindow().getStart() + 1);
             int delLength = 0;
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 730d57da4..f14c4e8c7 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
@@ -154,7 +154,8 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
     public double minCompQualScore = NO_MIN_QUAL_SCORE;
 
     // Right now we will only be looking at SNPS
-    EnumSet<VariantContext.Type> ALLOW_VARIANT_CONTEXT_TYPES = EnumSet.of(VariantContext.Type.SNP, VariantContext.Type.NO_VARIATION);
+    // todo -- enable INDEL variant contexts, there's no reason not to but the integration tests need to be updated
+    EnumSet<VariantContext.Type> ALLOW_VARIANT_CONTEXT_TYPES = EnumSet.of(VariantContext.Type.SNP, VariantContext.Type.NO_VARIATION); //, VariantContext.Type.INDEL);
 
     @Argument(shortName="rsID", fullName="rsID", doc="If provided, list of rsID and build number for capping known snps by their build date", required=false)
     protected String rsIDFile = null;