diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
index ba3909244..e65ea8023 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
@@ -51,7 +51,7 @@ public class ChromosomeCounts implements InfoFieldAnnotation, StandardAnnotation
             return null;
         
         Map<String, Object> map = new HashMap<String, Object>();
-        VariantContextUtils.calculateChromosomeCounts(vc, map, false);
+        VariantContextUtils.calculateChromosomeCounts(vc, map, true);
         return map;
     }