diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java
index a73e125ad..201028d99 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java
@@ -183,6 +183,10 @@ public class VariantEval extends RodWalker<Integer, Integer> implements TreeRedu
     @Argument(fullName="keepAC0", shortName="keepAC0", doc="If provided, modules that track polymorphic sites will not require that a site have AC > 0 when the input eval has genotypes", required=false)
     private boolean keepSitesWithAC0 = false;
 
+    @Hidden
+    @Argument(fullName="numSamples", shortName="numSamples", doc="If provided, modules that track polymorphic sites will not require that a site have AC > 0 when the input eval has genotypes", required=false)
+    private int numSamplesFromArgument = 0;
+
     /**
      * If true, VariantEval will treat -eval 1 -eval 2 as separate tracks from the same underlying
      * variant set, and evaluate the union of the results.  Useful when you want to do -eval chr1.vcf -eval chr2.vcf etc.
@@ -589,6 +593,14 @@ public class VariantEval extends RodWalker<Integer, Integer> implements TreeRedu
     public boolean isSubsettingToSpecificSamples() { return isSubsettingSamples; }
     public Set<String> getSampleNamesForEvaluation() { return sampleNamesForEvaluation; }
 
+    public int getNumberOfSamplesForEvaluation() {
+        if (sampleNamesForEvaluation!= null &&  !sampleNamesForEvaluation.isEmpty())
+            return sampleNamesForEvaluation.size();
+        else {
+            return numSamplesFromArgument;
+        }
+
+    }
     public Set<String> getSampleNamesForStratification() { return sampleNamesForStratification; }
 
     public List<RodBinding<VariantContext>> getComps() { return comps; }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java
index e6efd4482..7197fc14c 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java
@@ -29,7 +29,7 @@ public class AlleleCount extends VariantStratifier {
 
         // There are ploidy x n sample chromosomes
         // TODO -- generalize to handle multiple ploidy
-        nchrom = getVariantEvalWalker().getSampleNamesForEvaluation().size() * getVariantEvalWalker().getSamplePloidy();
+        nchrom = getVariantEvalWalker().getNumberOfSamplesForEvaluation() * getVariantEvalWalker().getSamplePloidy();
         if ( nchrom < 2 )
             throw new UserException.BadArgumentValue("AlleleCount", "AlleleCount stratification requires an eval vcf with at least one sample");