diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java
index 7ab3f81f0..5639ef30e 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java
@@ -197,14 +197,16 @@ public class Genotype {
         if ( alleles == null ) return;
         if ( alleles.size() == 0) throw new IllegalArgumentException("BUG: alleles cannot be of size 0");
 
-        int nNoCalls = 0;
+        // int nNoCalls = 0;
         for ( Allele allele : alleles ) {
             if ( allele == null )
                 throw new IllegalArgumentException("BUG: allele cannot be null in Genotype");
-            nNoCalls += allele.isNoCall() ? 1 : 0;
+            // nNoCalls += allele.isNoCall() ? 1 : 0;
         }
-        if ( nNoCalls > 0 && nNoCalls != alleles.size() )
-            throw new IllegalArgumentException("BUG: alleles include some No Calls and some Calls, an illegal state " + this);
+
+        // Technically, the spec does allow for the below case so this is not an illegal state
+        //if ( nNoCalls > 0 && nNoCalls != alleles.size() )
+        //    throw new IllegalArgumentException("BUG: alleles include some No Calls and some Calls, an illegal state " + this);
     }
 
     public String getGenotypeString() {
diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java
index 9026f09d6..a5060e54e 100755
--- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java
@@ -252,6 +252,23 @@ public class VariantContextUnitTest extends BaseTest {
         Assert.assertEquals(vc.getSampleNames().size(), 0);
     }
 
+    @Test
+    public void testCreatingPartiallyCalledGenotype() {
+        List<Allele> alleles = Arrays.asList(Aref, C);
+        Genotype g = new Genotype("foo", Arrays.asList(C, Allele.NO_CALL), 10);
+        VariantContext vc = new VariantContext("test", snpLoc, snpLocStart, snpLocStop, alleles, Arrays.asList(g));
+
+        Assert.assertTrue(vc.isSNP());
+        Assert.assertEquals(vc.getNAlleles(), 2);
+        Assert.assertTrue(vc.hasGenotypes());
+        Assert.assertFalse(vc.isMonomorphic());
+        Assert.assertTrue(vc.isPolymorphic());
+        Assert.assertEquals(vc.getGenotype("foo"), g);
+        Assert.assertEquals(vc.getChromosomeCount(), 2); // we know that there are 2 chromosomes, even though one isn't called
+        Assert.assertEquals(vc.getChromosomeCount(Aref), 0);
+        Assert.assertEquals(vc.getChromosomeCount(C), 1);
+    }
+
     @Test (expectedExceptions = IllegalArgumentException.class)
     public void testBadConstructorArgs1() {
         new VariantContext("test", insLoc, insLocStart, insLocStop, Arrays.asList(delRef, ATCref));