diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java
index 9056d917c..61991deba 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java
@@ -204,7 +204,7 @@ public class BeagleOutputToVCFWalker  extends RodWalker<Integer, Integer> {
             ArrayList<String> beagleGenotypePairs = beaglePhasedFeature.getGenotypes().get(sample);
 
             Allele originalAlleleA = g.getAllele(0);
-            Allele originalAlleleB = g.getAllele(1);
+            Allele originalAlleleB = (g.getAlleles().size() == 2) ? g.getAllele(1) : g.getAllele(0); // hack to deal with no-call genotypes
 
             // We have phased genotype in hp. Need to set the isRef field in the allele.
             List<Allele> alleles = new ArrayList<Allele>();
@@ -213,6 +213,9 @@ public class BeagleOutputToVCFWalker  extends RodWalker<Integer, Integer> {
             String alleleB = beagleGenotypePairs.get(1);
 
             byte[] r = alleleA.getBytes();
+
+            //System.out.println(context.getLocation() + " : " + alleleA + " " + alleleB);
+
             byte rA = r[0];
 
             Boolean isRefA = (refByte  == rA);
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ProduceBeagleInputWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ProduceBeagleInputWalker.java
index 8277469b4..8a7876cfa 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ProduceBeagleInputWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ProduceBeagleInputWalker.java
@@ -148,6 +148,26 @@ public class ProduceBeagleInputWalker extends RodWalker<Integer, Integer> {
                         beagleGenotypesWriter.format("%c %c ", a, b);
                     }
                 }
+                else if (genotype.isCalled() && !genotype.hasAttribute(VCFConstants.GENOTYPE_LIKELIHOODS_KEY)) {
+                    // hack to deal with input VCFs with no genotype likelihoods.  Just assume the called genotype
+                    // is confident.  This is useful for Hapmap and 1KG release VCFs.
+                    double AA = 0.02;
+                    double AB = 0.02;
+                    double BB = 0.02;
+
+                    if (genotype.isHomRef()) { AA = 0.96; }
+                    else if (genotype.isHet()) { AB = 0.96; }
+                    else if (genotype.isHomVar()) { BB = 0.96; }
+
+                    beagleWriter.printf("%.2f %.2f %.2f ", AA, AB, BB);
+
+                    if (beagleGenotypesWriter != null) {
+                        char a = genotype.getAllele(0).toString().charAt(0);
+                        char b = genotype.getAllele(0).toString().charAt(0);
+
+                        beagleGenotypesWriter.format("%c %c ", a, b);
+                    }
+                }
                 else  {
                     beagleWriter.print("0.33 0.33 0.33 "); // write 1/3 likelihoods for uncalled genotypes.
                     if (beagleGenotypesWriter != null)