diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
index ff56bd9a8..15278bef8 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
@@ -11,31 +11,32 @@ import java.util.ArrayList;
 public class AlleleBalance implements VariantAnnotation {
 
     public Pair<String, String> annotate(ReferenceContext ref, ReadBackedPileup pileup, List<Genotype> genotypes) {
-        double ratio = -1;
 
-        if ( genotypes.size() > 0 ) {
-            Genotype g = genotypes.get(0);
-            if ( g instanceof ReadBacked && g instanceof PosteriorsBacked ) {
-                Pair<Double, Integer> weightedBalance = computeWeightedBalance(ref.getBase(), genotypes, pileup);
-                if ( weightedBalance.second == 0 )
-                    return null;
-                ratio = weightedBalance.first;
-            } else {
-                // this test doesn't make sense for homs
-                Genotype genotype = VariantAnnotator.getFirstHetVariant(genotypes);
-                if ( genotype == null )
-                    return null;
+        if ( genotypes.size() == 0 )
+            return null;
 
-                final String genotypeStr = genotype.getBases().toUpperCase();
-                if ( genotypeStr.length() != 2 )
-                    return null;
+        double ratio;
+        Genotype g = genotypes.get(0);
+        if ( g instanceof ReadBacked && g instanceof PosteriorsBacked ) {
+            Pair<Double, Integer> weightedBalance = computeWeightedBalance(ref.getBase(), genotypes, pileup);
+            if ( weightedBalance.second == 0 )
+                return null;
+            ratio = weightedBalance.first;
+        } else {
+            // this test doesn't make sense for homs
+            Genotype genotype = VariantAnnotator.getFirstHetVariant(genotypes);
+            if ( genotype == null )
+                return null;
 
-                final String bases = pileup.getBasesAsString().toUpperCase();
-                if ( bases.length() == 0 )
-                    return null;
+            final String genotypeStr = genotype.getBases().toUpperCase();
+            if ( genotypeStr.length() != 2 )
+                return null;
 
-                ratio = computeSingleBalance(ref.getBase(), genotypeStr, bases);
-            }
+            final String bases = pileup.getBasesAsString().toUpperCase();
+            if ( bases.length() == 0 )
+                return null;
+
+            ratio = computeSingleBalance(ref.getBase(), genotypeStr, bases);
         }
 
         return new Pair<String, String>("AlleleBalance", String.format("%.2f", ratio));
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/OnOffGenotype.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/OnOffGenotype.java
index 6e97470fa..17b945dba 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/OnOffGenotype.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/OnOffGenotype.java
@@ -14,30 +14,30 @@ public class OnOffGenotype implements VariantAnnotation {
 
     public Pair<String, String> annotate(ReferenceContext ref, ReadBackedPileup pileup, List<Genotype> genotypes) {
 
-        double ratio = -1;
+        if ( genotypes.size() == 0 )
+            return null;
 
-        if ( genotypes.size() > 0 ) {
-            Genotype g = genotypes.get(0);
-            if ( g instanceof ReadBacked && g instanceof PosteriorsBacked) {
-                Pair<Double, Integer> weightedBalance = computeWeightedBalance(ref.getBase(), genotypes, pileup);
-                if ( weightedBalance.second == 0 )
-                    return null;
-                ratio = weightedBalance.first;
-            } else {
-                Genotype genotype = VariantAnnotator.getFirstVariant(ref.getBase(), genotypes);
-                if ( genotype == null )
-                    return null;
+        double ratio;
+        Genotype g = genotypes.get(0);
+        if ( g instanceof ReadBacked && g instanceof PosteriorsBacked) {
+            Pair<Double, Integer> weightedBalance = computeWeightedBalance(ref.getBase(), genotypes, pileup);
+            if ( weightedBalance.second == 0 )
+                return null;
+            ratio = weightedBalance.first;
+        } else {
+            Genotype genotype = VariantAnnotator.getFirstVariant(ref.getBase(), genotypes);
+            if ( genotype == null )
+                return null;
 
-                final String genotypeStr = genotype.getBases().toUpperCase();
-                if ( genotypeStr.length() != 2 )
-                    return null;
+            final String genotypeStr = genotype.getBases().toUpperCase();
+            if ( genotypeStr.length() != 2 )
+                return null;
 
-                final String bases = pileup.getBasesAsString().toUpperCase();
-                if ( bases.length() == 0 )
-                    return null;
+            final String bases = pileup.getBasesAsString().toUpperCase();
+            if ( bases.length() == 0 )
+                return null;
 
-                ratio = computeSingleBalance(genotypeStr, bases);
-            }
+            ratio = computeSingleBalance(genotypeStr, bases);
         }
 
         return new Pair<String, String>("OnOffGenotype", String.format("%.2f", ratio));
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/JointEstimateGenotypeCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/JointEstimateGenotypeCalculationModel.java
index 5dce2fea7..c578eb0ec 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/JointEstimateGenotypeCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/JointEstimateGenotypeCalculationModel.java
@@ -238,6 +238,8 @@ public abstract class JointEstimateGenotypeCalculationModel extends GenotypeCalc
         }
 
         double phredScaledConfidence = -10.0 * Math.log10(alleleFrequencyPosteriors[indexOfMax][0]);
+        if ( Double.isInfinite(phredScaledConfidence) )
+            phredScaledConfidence = -10.0 * log10PofDgivenAFi[indexOfMax][0];
         int bestAFguess = Utils.findIndexOfMaxEntry(alleleFrequencyPosteriors[indexOfMax]);
 
         // return a null call if we don't pass the confidence cutoff or the most likely allele frequency is zero