diff --git a/java/src/org/broadinstitute/sting/utils/BasicPileup.java b/java/src/org/broadinstitute/sting/utils/BasicPileup.java
index 58b119649..5dcb36df0 100755
--- a/java/src/org/broadinstitute/sting/utils/BasicPileup.java
+++ b/java/src/org/broadinstitute/sting/utils/BasicPileup.java
@@ -190,7 +190,7 @@ abstract public class BasicPileup implements Pileup {
 
         if (sbases == null) { return null; }
 
-        ArrayList<Byte> pbases = basePileup(reads, offsets);
+        ArrayList<Byte> pbases = basePileup(reads, offsets,true);
 
         Random generator = new Random();