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 acf56d6ca..6418915ad 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/JointEstimateGenotypeCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/JointEstimateGenotypeCalculationModel.java
@@ -47,15 +47,26 @@ public abstract class JointEstimateGenotypeCalculationModel extends GenotypeCalc
 
         // find the alternate allele with the largest sum of quality scores
         initializeBestAlternateAllele(ref, context);
-        // if there are no non-ref bases and we don't want all bases, then we can just return
-        if ( !ALL_BASE_MODE && bestAlternateAllele == null )
-            return new Pair<VariationCall, List<Genotype>>(null, null);
 
-        initializeAlleleFrequencies(frequencyEstimationPoints);
+        // if there are no non-ref bases...
+        if ( bestAlternateAllele == null ) {
+            // if we don't want all bases, then we can just return
+            if ( !ALL_BASE_MODE )
+                return new Pair<VariationCall, List<Genotype>>(null, null);
 
-        initialize(ref, contexts, StratifiedContext.OVERALL);
-        calculateAlleleFrequencyPosteriors(ref, frequencyEstimationPoints, contexts, StratifiedContext.OVERALL);
-        calculatePofFs(ref, frequencyEstimationPoints);
+            // otherwise, we care about the ref base
+            bestAlternateAllele = ref;
+
+            // TODO -- figure out what to do here!
+
+        }
+        else {
+            initializeAlleleFrequencies(frequencyEstimationPoints);
+
+            initialize(ref, contexts, StratifiedContext.OVERALL);
+            calculateAlleleFrequencyPosteriors(ref, frequencyEstimationPoints, contexts, StratifiedContext.OVERALL);
+            calculatePofFs(ref, frequencyEstimationPoints);
+        }
 
         // print out stats if we have a writer
         if ( verboseWriter != null )
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java
index 7f4bb4689..ed32e51ae 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java
@@ -30,7 +30,7 @@ import java.util.*;
 public class VariantEvalWalker extends RefWalker<Integer, Integer> {
 //public class VariantEvalWalker extends RodWalker<Integer, Integer> {
     @Argument(shortName="minPhredConfidenceScore", doc="Minimum confidence score to consider an evaluation SNP a variant", required=false)
-    public int minConfidenceScore = -1;
+    public double minConfidenceScore = -1.0;
 
     @Argument(shortName="printVariants", doc="If true, prints the variants in all of the variant tracks that are examined", required=false)
     public boolean printVariants = false;