diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
index 644a916b2..9fc7879f8 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
@@ -15,7 +15,7 @@ public class AlleleBalance extends StandardVariantAnnotation {
 
     public String annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, Variation variation) {
 
-        if ( !(variation instanceof VariantBackedByGenotype) )
+        if ( !variation.isBiallelic() || !(variation instanceof VariantBackedByGenotype) )
             return null;
         final List<Genotype> genotypes = ((VariantBackedByGenotype)variation).getGenotypes();
         if ( genotypes == null || genotypes.size() == 0 )
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
index 3989d317d..b3abbd9ac 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
@@ -20,8 +20,9 @@ public class RankSumTest implements VariantAnnotation {
 
     public String annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, Variation variation) {
 
-        if ( !(variation instanceof VariantBackedByGenotype) )
+        if ( !variation.isBiallelic() || !variation.isSNP() || !(variation instanceof VariantBackedByGenotype) )
             return null;
+        
         final List<Genotype> genotypes = ((VariantBackedByGenotype)variation).getGenotypes();
         if ( genotypes == null || genotypes.size() == 0 )
             return null;
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 f6eac214e..581682542 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
@@ -162,10 +162,8 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
         Map<String, String> annotations = new HashMap<String, String>();
         VariationRod variant = (VariationRod)rods.getRecords().get(0);
 
-        // if the reference base is not ambiguous, the variant is a SNP, and it's the appropriate type, we can annotate
-        if ( BaseUtils.simpleBaseToBaseIndex(ref.getBase()) != -1 &&
-                variant.isBiallelic() &&
-                variant.isSNP() ) {
+        // if the reference base is not ambiguous, we can annotate
+        if ( BaseUtils.simpleBaseToBaseIndex(ref.getBase()) != -1 ) {
             Map<String, StratifiedAlignmentContext> stratifiedContexts = StratifiedAlignmentContext.splitContextBySample(context.getBasePileup());
             if ( stratifiedContexts != null )
                 annotations = getAnnotations(tracker, ref, stratifiedContexts, variant, requestedAnnotations);
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
index 1a4aa3d25..4a82cbbc1 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
@@ -66,7 +66,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testHasAnnotsAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -standard -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("ad0d78f399bba23227cf07341708e27d"));
+                Arrays.asList("e3282acfec015441dfc38715d5bfe530"));
         executeTest("test file has annotations, asking for annotations, #1", spec);
     }
 
@@ -98,7 +98,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testNoAnnotsAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -standard -B variant,VCF," + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("b8609ff527e0882dfbe3505357fd2705"));
+                Arrays.asList("20943a3666ceef605d9154b6f2ff2fa1"));
         executeTest("test file doesn't have annotations, asking for annotations, #1", spec);
     }
 
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
index fec835294..7ee1d6022 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
@@ -22,7 +22,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testMultiSamplePilot1PointEM() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,023,400-10,024,000 -bm empirical -gm EM_POINT_ESTIMATE -confidence 30", 1,
-                Arrays.asList("b7ea2739f9190ea6c5c63ffd1150454e"));
+                Arrays.asList("ee02dbbbbe957ccf0ee79dcdfd7abff6"));
         executeTest("testMultiSamplePilot1 - Point Estimate EM", spec);
     }