diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java
index 46aa6d0f3..761251259 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java
@@ -59,6 +59,8 @@ public class BaseCounts extends InfoFieldAnnotation {
         int[] counts = new int[4];
 
         for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() ) {
+            if ( !sample.getValue().hasBasePileup() )
+                continue;
             for (byte base : sample.getValue().getBasePileup().getBases() ) {
                 int index = BaseUtils.simpleBaseToBaseIndex(base);
                 if ( index != -1 )