diff --git a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
index c54f10aaa..230d1b892 100755
--- a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
+++ b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
@@ -112,31 +112,36 @@ public class VariantContextUtils {
 
         // if there are alternate alleles, record the relevant tags
         if ( vc.getAlternateAlleles().size() > 0 ) {
-            ArrayList<Double> alleleFreqs = new ArrayList<Double>();
+            ArrayList<String> alleleFreqs = new ArrayList<String>();
             ArrayList<Integer> alleleCounts = new ArrayList<Integer>();
+            double totalChromosomes = (double)vc.getChromosomeCount();
             for ( Allele allele : vc.getAlternateAlleles() ) {
-                alleleCounts.add(vc.getChromosomeCount(allele));
-                alleleFreqs.add((double)vc.getChromosomeCount(allele) / (double)vc.getChromosomeCount());
+                int altChromosomes = vc.getChromosomeCount(allele);
+                alleleCounts.add(altChromosomes);
+                String freq = String.format(makePrecisionFormatStringFromDenominatorValue(totalChromosomes), ((double)altChromosomes / totalChromosomes));
+                alleleFreqs.add(freq);
             }
 
             attributes.put(VCFConstants.ALLELE_COUNT_KEY, alleleCounts);
             attributes.put(VCFConstants.ALLELE_FREQUENCY_KEY, alleleFreqs);
         }
-
-//        // otherwise, remove them if present and requested
-//        else if ( removeStaleValues ) {
-//            if ( attributes.containsKey(VCFConstants.ALLELE_COUNT_KEY) )
-//                attributes.remove(VCFConstants.ALLELE_COUNT_KEY);
-//            if ( attributes.containsKey(VCFConstants.ALLELE_FREQUENCY_KEY) )
-//                attributes.remove(VCFConstants.ALLELE_FREQUENCY_KEY);
-//        }
-        // otherwise, set them to 0
         else {
             attributes.put(VCFConstants.ALLELE_COUNT_KEY, 0);
             attributes.put(VCFConstants.ALLELE_FREQUENCY_KEY, 0.0);
         }
     }
 
+    private static String makePrecisionFormatStringFromDenominatorValue(double maxValue) {
+        int precision = 1;
+
+        while ( maxValue > 1 ) {
+            precision++;
+            maxValue /= 10.0;
+        }
+
+        return "%." + precision + "f";
+    }
+
     /**
      * A simple but common wrapper for matching VariantContext objects using JEXL expressions
      */
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedArgumentCollection.java
index 1f66afe83..8478b2d65 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedArgumentCollection.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedArgumentCollection.java
@@ -79,7 +79,7 @@ public class UnifiedArgumentCollection {
 
     // control the various parameters to be used
     @Argument(fullName = "min_base_quality_score", shortName = "mbq", doc = "Minimum base quality required to consider a base for calling", required = false)
-    public int MIN_BASE_QUALTY_SCORE = 20;
+    public int MIN_BASE_QUALTY_SCORE = 17;
 
     @Argument(fullName = "min_mapping_quality_score", shortName = "mmq", doc = "Minimum read mapping quality required to consider a read for calling", required = false)
     public int MIN_MAPPING_QUALTY_SCORE = 20;
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
index 3d737500f..776f61362 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
@@ -25,7 +25,7 @@ public class
     public void testMultiSamplePilot1Joint() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000", 1,
-                Arrays.asList("9870dd089d0f76c8dd3e74bc9f2ba0f0"));
+                Arrays.asList("1dde074afe990fd38941de18bd35e188"));
         executeTest("testMultiSamplePilot1 - Joint Estimate", spec);
     }