diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
index dedd2f26e..ba9a10d8b 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
@@ -112,26 +112,29 @@ public class VariantContextAdaptors {
                 alleles.add(refAllele);
 
                 // add all of the alt alleles
+                boolean sawNullAllele = false;
                 for ( String alt : DbSNPHelper.getAlternateAlleleList(dbsnp) ) {
                     if ( ! Allele.acceptableAlleleBases(alt) ) {
                         //System.out.printf("Excluding dbsnp record %s%n", dbsnp);
                         return null;
                     }
-                    alleles.add(Allele.create(alt, false));
+                    Allele altAllele = Allele.create(alt, false);
+                    alleles.add(altAllele);
+                    if ( altAllele.isNull() )
+                        sawNullAllele = true;
                 }
 
                 Map<String, Object> attributes = new HashMap<String, Object>();
                 attributes.put(VariantContext.ID_KEY, dbsnp.getRsID());
 
-                boolean vcIsDeletion = DbSNPHelper.isDeletion(dbsnp) || DbSNPHelper.isComplexIndel(dbsnp);
-                if ( vcIsDeletion ) {
+                if ( sawNullAllele ) {
                     int index = dbsnp.getStart() - ref.getWindow().getStart() - 1;
                     if ( index < 0 )
                         return null; // we weren't given enough reference context to create the VariantContext
                     attributes.put(VariantContext.REFERENCE_BASE_FOR_INDEL_KEY, new Byte(ref.getBases()[index]));
                 }
                 Collection<Genotype> genotypes = null;
-                VariantContext vc = new VariantContext(name, dbsnp.getChr(), dbsnp.getStart() - (vcIsDeletion ? 1 : 0),dbsnp.getEnd(), alleles, genotypes, VariantContext.NO_NEG_LOG_10PERROR, null, attributes);
+                VariantContext vc = new VariantContext(name, dbsnp.getChr(), dbsnp.getStart() - (sawNullAllele ? 1 : 0),dbsnp.getEnd(), alleles, genotypes, VariantContext.NO_NEG_LOG_10PERROR, null, attributes);
                 return vc;
             } else
                 return null; // can't handle anything else
diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java
index ced2bf00b..6ed00f0ea 100755
--- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java
@@ -58,7 +58,7 @@ public class VariantContextIntegrationTest extends WalkerTest {
         // this really just tests that we are seeing the same number of objects over all of chr1
         WalkerTestSpec spec = new WalkerTestSpec( root + " -L 1" + " -o %s",
                 1, // just one output file
-                Arrays.asList("2532234d2c934a5e14849655dd7b5f4f"));
+                Arrays.asList("045a5b02c86aeb9301dc0b724da0c8f7"));
          executeTest("testLargeScaleConversion", spec);
     }
 }