diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
index 9947ea054..d6f82245a 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
@@ -460,6 +460,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
 
             //logger.debug(consensus.str +  " " + consensus.mismatchSum);
             if ( bestConsensus == null || bestConsensus.mismatchSum > consensus.mismatchSum) {
+                if ( bestConsensus != null ) bestConsensus.readIndexes.clear();
                 bestConsensus = consensus;
                 //logger.debug(consensus.str +  " " + consensus.mismatchSum);
             } else {
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerWalker.java
index b7caee706..390a80c21 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerWalker.java
@@ -365,6 +365,7 @@ public class  IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
 
             //logger.debug(consensus.str +  " " + consensus.mismatchSum);
             if ( bestConsensus == null || bestConsensus.mismatchSum > consensus.mismatchSum) {
+                if ( bestConsensus != null ) bestConsensus.readIndexes.clear();
                 bestConsensus = consensus;
                 //logger.debug(consensus.str +  " " + consensus.mismatchSum);
             } else {