diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
index 8c281b2f8..87b8bac1d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
@@ -93,28 +93,35 @@ public class CountVariants extends VariantEvaluator implements StandardEval {
     public String update1(VariantContext vc1, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
         nCalledLoci++;
 
-        if (vc1.isVariant()) nVariantLoci++;
-        switch (vc1.getType()) {
-            case NO_VARIATION:
-                nRefLoci++;
-                break;
-            case SNP:
-                nSNPs++;
-                if (vc1.getAttributeAsBoolean("ISSINGLETON")) nSingletons++;
-                break;
-            case MNP:
-                nMNPs++;
-                if (vc1.getAttributeAsBoolean("ISSINGLETON")) nSingletons++;
-                break;
-            case INDEL:
-                if (vc1.isInsertion()) nInsertions++;
-                else nDeletions++;
-                break;
-            case MIXED:
-                nComplex++;
-                break;
-            default:
-                throw new ReviewedStingException("Unexpected VariantContext type " + vc1.getType());
+        // Note from Eric:
+        // This is really not correct.  What we really want here is a polymorphic vs. monomorphic count (i.e. on the Genotypes).
+        // So in order to maintain consistency with the previous implementation (and the intention of the original author), I've
+        // added in a proxy check for monomorphic status here.
+        if ( !vc1.isVariant() || (vc1.hasGenotypes() && vc1.getHomRefCount() == vc1.getNSamples()) ) {
+            nRefLoci++;
+        } else {
+            nVariantLoci++;
+            switch (vc1.getType()) {
+                case NO_VARIATION:
+                    break;
+                case SNP:
+                    nSNPs++;
+                    if (vc1.getAttributeAsBoolean("ISSINGLETON")) nSingletons++;
+                    break;
+                case MNP:
+                    nMNPs++;
+                    if (vc1.getAttributeAsBoolean("ISSINGLETON")) nSingletons++;
+                    break;
+                case INDEL:
+                    if (vc1.isInsertion()) nInsertions++;
+                    else nDeletions++;
+                    break;
+                case MIXED:
+                    nComplex++;
+                    break;
+                default:
+                    throw new ReviewedStingException("Unexpected VariantContext type " + vc1.getType());
+            }
         }
 
         String refStr = vc1.getReference().getBaseString().toUpperCase();
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
index 17bb70c00..33fb008ca 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
@@ -280,7 +280,7 @@ public class VariantEvalUtils {
      * @return a new VariantContext with just the requested samples
      */
     public VariantContext getSubsetOfVariantContext(VariantContext vc, Collection<String> sampleNames) {
-        VariantContext vcsub = vc.subContextFromGenotypes(vc.getGenotypes(sampleNames).values());
+        VariantContext vcsub = vc.subContextFromGenotypes(vc.getGenotypes(sampleNames).values(), vc.getAlleles());
 
         HashMap<String, Object> newAts = new HashMap<String, Object>(vcsub.getAttributes());
 
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
index 72af7034b..1de9a72d8 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
@@ -236,7 +236,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                 " --eval " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" +
                 " --comp:comp_genotypes,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.head.vcf";
         WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -ST CpG -o %s",
-                1, Arrays.asList("14054badcd89b24c2375e1d09918f681"));
+                1, Arrays.asList("125fe0a04b5d933cc14016598b2791cd"));
         executeTestParallel("testSelect1", spec);
     }