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 a344817a0..6ed00f0ea 100755
--- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java
@@ -19,14 +19,14 @@ public class VariantContextIntegrationTest extends WalkerTest {
 
     static HashMap<String, String> expectations = new HashMap<String, String>();
     static {
-        expectations.put("-L 1:1-10000 --printPerLocus", "e4ee2eaa3114888e918a1c82df7a027a");
-        expectations.put("-L 1:1-10000 --printPerLocus --takeFirstOnly", "5b5635e4877d82e8a27d70dac24bda2f");
-        expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsStartinAtCurrentPosition", "ceced3f270b4fe407ee83bc9028becde");
-        expectations.put("-L 1:1-10000 --printPerLocus --takeFirstOnly --onlyContextsStartinAtCurrentPosition", "9a9b9e283553c28bf58de1cafa38fe92");
+        expectations.put("-L 1:1-10000 --printPerLocus", "e9d96677a57bc3a10fb6d9ba942c19f0");
+        expectations.put("-L 1:1-10000 --printPerLocus --takeFirstOnly", "8a1174d2b18b98e624abbe93e6af8fdd");
+        expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsStartinAtCurrentPosition", "3933f1fae5453c54c3f791a23de07599");
+        expectations.put("-L 1:1-10000 --printPerLocus --takeFirstOnly --onlyContextsStartinAtCurrentPosition", "c9cf2f01bf045a58dcc7649fd6ea2396");
         expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType SNP", "2097e32988d603d3b353b50218c86d3b");
-        expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType INDEL", "033bd952fca048fe1a4f6422b57ab2ed");
-        expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType INDEL --onlyContextsStartinAtCurrentPosition", "5e40980c02797f90821317874426a87a");
-        expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType MIXED", "e5a00766f8c1ff9cf92310bafdec3126");
+        expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType INDEL", "a103d856e8bc558c949c6e3f184e8913");
+        expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType INDEL --onlyContextsStartinAtCurrentPosition", "5f2265ac6c6d80d64dc6e69a05c1250b");
+        expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType MIXED", "06a3ae4c0afa23b429a9491ab7707f3c");
         expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType NO_VARIATION", "39335acdb34c8a2af433dc50d619bcbc");
     }
 
@@ -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("529f936aa6c303658b23caf4e527782f"));
+                Arrays.asList("045a5b02c86aeb9301dc0b724da0c8f7"));
          executeTest("testLargeScaleConversion", spec);
     }
 }