We already had isPolymorphic and isMonomorphic in the VariantContext, but the implementation was incorrect for many edge cases (e.g. sites-only files, sites with samples who were no-called). Fixing. Moving on to VE now.

public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java

@@ -983,7 +983,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
      * @return true if it's monomorphic
      */
     public boolean isMonomorphic() {
-        return ! isVariant() || getChromosomeCount(getReference()) == getChromosomeCount();
+        return ! isVariant() || (hasGenotypes() && getHomRefCount() + getNoCallCount() == getNSamples());
     }
 
     /**