diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
index a80ebc3f8..75d8e05b7 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
@@ -72,7 +72,7 @@ public abstract class RankSumTest implements InfoFieldAnnotation, ExperimentalAn
         }
 
         final Map<String, Object> map = new HashMap<String, Object>();
-        map.put(getKeyNames().get(0), String.format("%.3f", QualityUtils.phredScaleErrorRate(pvalue)));
+        map.put(getKeyNames().get(0), String.format("%.3f", Math.abs(QualityUtils.phredScaleErrorRate(pvalue))));
         return map;
     }
 
diff --git a/java/src/org/broadinstitute/sting/utils/WilcoxonRankSum.java b/java/src/org/broadinstitute/sting/utils/WilcoxonRankSum.java
index bb925104c..5ba70e9a7 100755
--- a/java/src/org/broadinstitute/sting/utils/WilcoxonRankSum.java
+++ b/java/src/org/broadinstitute/sting/utils/WilcoxonRankSum.java
@@ -124,8 +124,9 @@ public class WilcoxonRankSum {
     // calculate normal approximation of the p-value
     // returns -1 when unable to calculate it (too few data points)
     public double getPValue(WILCOXON_H0 h0) {
-        if ( observations.size() == 0 )
+        if ( observations.size() == 0 ) {
             return -1.0;
+        }
 
         // dither to break rank ties
         dither();
@@ -144,6 +145,11 @@ public class WilcoxonRankSum {
         }
         int n2 = observations.size() - n1;
 
+        if ( n1 == 0 || n2 == 0 ) {
+            // one of the sets is empty so there is no information
+            return -1.0;
+        }
+
         // todo -- these are actually integers
         // we want the smaller of U1 and U2
         double U1 = sum - (n1 * (n1 + 1.0) / 2.0);