diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCompoundHeaderLine.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCompoundHeaderLine.java
index 6f9a8f5e6..667de3dea 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCompoundHeaderLine.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCompoundHeaderLine.java
@@ -75,22 +75,24 @@ public abstract class VCFCompoundHeaderLine extends VCFHeaderLine implements VCF
      * If the count is a fixed count, return that.  For example, a field with size of 1 in the header returns 1
      * If the count is of type A, return vc.getNAlleles - 1
      * If the count is of type G, return the expected number of genotypes given the number of alleles in VC and the
-     *   max ploidy among all samples
+     *   max ploidy among all samples.  Note that if the max ploidy of the VC is 0 (there's no GT information
+     *   at all, then implicitly assume diploid samples when computing G values.
      * If the count is UNBOUNDED return -1
      *
      * @param vc
      * @return
      */
     public int getCount(final VariantContext vc) {
-        int myCount;
         switch ( countType ) {
-            case INTEGER: myCount = count; break;
-            case UNBOUNDED: myCount = -1; break;
-            case A: myCount = vc.getNAlleles() - 1; break;
-            case G: myCount = GenotypeLikelihoods.numLikelihoods(vc.getNAlleles(), vc.getMaxPloidy()); break;
-            default: throw new ReviewedStingException("Unknown count type: " + countType);
+            case INTEGER:       return count;
+            case UNBOUNDED:     return -1;
+            case A:             return vc.getNAlleles() - 1;
+            case G:
+                final int ploidy = vc.getMaxPloidy();
+                return GenotypeLikelihoods.numLikelihoods(vc.getNAlleles(), ploidy == 0 ? 2 : ploidy);
+            default:
+                throw new ReviewedStingException("Unknown count type: " + countType);
         }
-        return myCount;
     }
 
     public void setNumberToUnbounded() {
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java
index bb4a5abb9..d644eda7d 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java
@@ -363,13 +363,11 @@ public class GenotypeLikelihoods {
      *   S(N,1) = N  (only way to have N integers add up to 1 is all-zeros except one element with a one. There are N of these vectors)
      *   S(1,P) = 1 (only way to have 1 integer add to P is with that integer P itself).
      *
-     * note that in the case where ploidy == 0 we assume that the ploidy actually == 2
-     *
      *   @param  numAlleles      Number of alleles (including ref)
      *   @param  ploidy          Ploidy, or number of chromosomes in set
      *   @return    Number of likelihood elements we need to hold.
      */
-    @Requires({"ploidy >= 0", "numAlleles > 0"})
+    @Requires({"ploidy > 0", "numAlleles > 0"})
     @Ensures("result > 0")
     public static int numLikelihoods(final int numAlleles, final int ploidy) {
         if ( numAlleles < NUM_LIKELIHOODS_CACHE_N_ALLELES