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 5639ef30e..e2e44e2b9 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java
@@ -108,14 +108,19 @@ public class Genotype {
     /**
      * @return the ploidy of this genotype
      */
-    public int getPloidy() { return alleles.size(); }
+    public int getPloidy() {
+        if ( alleles == null )
+            throw new ReviewedStingException("Requesting ploidy for an UNAVAILABLE genotype");
+        return alleles.size();
+    }
 
     public enum Type {
         NO_CALL,
         HOM_REF,
         HET,
         HOM_VAR,
-        UNAVAILABLE
+        UNAVAILABLE,
+        MIXED  // no-call and call in the same genotype
     }
 
     public Type getType() {
@@ -129,36 +134,68 @@ public class Genotype {
         if ( alleles == null )
             return Type.UNAVAILABLE;
 
-        Allele firstAllele = alleles.get(0);
+        boolean sawNoCall = false, sawMultipleAlleles = false;
+        Allele observedAllele = null;
 
-        if ( firstAllele.isNoCall() ) {
-            return Type.NO_CALL;
+        for ( Allele allele : alleles ) {
+            if ( allele.isNoCall() )
+                sawNoCall = true;
+            else if ( observedAllele == null )
+                observedAllele = allele;
+            else if ( !allele.equals(observedAllele) )
+                sawMultipleAlleles = true;
         }
 
-        for (Allele a : alleles) {
-            if ( ! firstAllele.equals(a) )
-                return Type.HET;
+        if ( sawNoCall ) {
+            if ( observedAllele == null )
+                return Type.NO_CALL;
+            return Type.MIXED;
         }
-        return firstAllele.isReference() ? Type.HOM_REF : Type.HOM_VAR;
+
+        if ( observedAllele == null )
+            throw new ReviewedStingException("BUG: there are no alleles present in this genotype but the alleles list is not null");
+
+        return sawMultipleAlleles ? Type.HET : observedAllele.isReference() ? Type.HOM_REF : Type.HOM_VAR;
     }
 
     /**
-     * @return true if all observed alleles are the same (regardless of whether they are ref or alt)
+     * @return true if all observed alleles are the same (regardless of whether they are ref or alt); if any alleles are no-calls, this method will return false.
      */
     public boolean isHom()    { return isHomRef() || isHomVar(); }
+
+    /**
+     * @return true if all observed alleles are ref; if any alleles are no-calls, this method will return false.
+     */
     public boolean isHomRef() { return getType() == Type.HOM_REF; }
+
+    /**
+     * @return true if all observed alleles are alt; if any alleles are no-calls, this method will return false.
+     */
     public boolean isHomVar() { return getType() == Type.HOM_VAR; }
     
     /**
-     * @return true if we're het (observed alleles differ)
+     * @return true if we're het (observed alleles differ); if the ploidy is less than 2 or if any alleles are no-calls, this method will return false.
      */
     public boolean isHet() { return getType() == Type.HET; }
 
     /**
-     * @return true if this genotype is not actually a genotype but a "no call" (e.g. './.' in VCF)
+     * @return true if this genotype is not actually a genotype but a "no call" (e.g. './.' in VCF); if any alleles are not no-calls (even if some are), this method will return false.
      */
     public boolean isNoCall() { return getType() == Type.NO_CALL; }
+
+    /**
+     * @return true if this genotype is comprised of any alleles that are not no-calls (even if some are).
+     */
     public boolean isCalled() { return getType() != Type.NO_CALL && getType() != Type.UNAVAILABLE; }
+
+    /**
+     * @return true if this genotype is comprised of both calls and no-calls.
+     */
+    public boolean isMixed() { return getType() == Type.MIXED; }
+
+    /**
+     * @return true if the type of this genotype is set.
+     */
     public boolean isAvailable() { return getType() != Type.UNAVAILABLE; }
 
     //
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
index 14a680af4..f52a7087b 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
@@ -998,7 +998,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
                 else if ( g.isHomVar() )
                     genotypeCounts[Genotype.Type.HOM_VAR.ordinal()]++;
                 else
-                    throw new IllegalStateException("Genotype of unknown type: " + g);
+                    genotypeCounts[Genotype.Type.MIXED.ordinal()]++;
             }
         }
     }
@@ -1042,6 +1042,15 @@ public class VariantContext implements Feature { // to enable tribble intergrati
         return genotypeCounts[Genotype.Type.HOM_VAR.ordinal()];
     }
 
+    /**
+     * Genotype-specific functions -- how many mixed calls are there in the genotypes?
+     *
+     * @return number of mixed calls
+     */
+    public int getMixedCount() {
+        return genotypeCounts[Genotype.Type.MIXED.ordinal()];
+    }
+
     // ---------------------------------------------------------------------------------------------------------
     //
     // validation: extra-strict validation routines for paranoid users
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 a5060e54e..a4d78b637 100755
--- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java
@@ -267,6 +267,12 @@ public class VariantContextUnitTest extends BaseTest {
         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);
+        Assert.assertFalse(vc.getGenotype("foo").isHet());
+        Assert.assertFalse(vc.getGenotype("foo").isHom());
+        Assert.assertFalse(vc.getGenotype("foo").isNoCall());
+        Assert.assertFalse(vc.getGenotype("foo").isHom());
+        Assert.assertTrue(vc.getGenotype("foo").isMixed());
+        Assert.assertEquals(vc.getGenotype("foo").getType(), Genotype.Type.MIXED);
     }
 
     @Test (expectedExceptions = IllegalArgumentException.class)