diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index f385609b4..5c10ad654 100755
--- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
@@ -77,7 +77,7 @@ public class GenomeAnalysisEngine {
         if (argCollection.HAPMAPChipFile != null)
             bindConvenienceRods("hapmap-chip", "GFF", argCollection.HAPMAPChipFile);
         if ( argCollection.intervals != null )
-            bindConvenienceRods("interval", "Intervals", argCollection.intervals);
+            bindConvenienceRods("interval", "Intervals", argCollection.intervals.replaceAll(",", ""));
 
         // parse out the rod bindings
         ReferenceOrderedData.parseBindings(logger, argCollection.RODBindings, rods);
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantCounter.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantCounter.java
index 5bffd4274..9cc18cb15 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantCounter.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantCounter.java
@@ -26,8 +26,8 @@ public class VariantCounter extends BasicVariantAnalysis {
         List<String> s = new ArrayList<String>();
         s.add(String.format("n bases covered: %d", nBasesCovered));
         s.add(String.format("sites: %d", nSNPs));
-        s.add(String.format("variant rate: %.5f confident variants per base", nSNPs / (1.0 * nBasesCovered)));
-        s.add(String.format("variant rate: 1 / %d confident variants per base", nBasesCovered / nSNPs));
+        s.add(String.format("variant rate: %.5f confident variants per base", nSNPs / (1.0 * Math.max(nBasesCovered, 1))));
+        s.add(String.format("variant rate: 1 / %d confident variants per base", nBasesCovered / Math.max(nSNPs, 1)));
         return s;
     }
 }
\ No newline at end of file