diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalCleanerWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalCleanerWalker.java
index 6f60b1162..b51bd0ee7 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalCleanerWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalCleanerWalker.java
@@ -529,7 +529,7 @@ public class  IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
         }
                 
         logger.debug("Original mismatch columns = " + originalMismatchColumns + "; cleaned mismatch columns = " + cleanedMismatchColumns);
-        //out.println("Original mismatch columns = " + originalMismatchColumns + "; cleaned mismatch columns = " + cleanedMismatchColumns);
+        //out.println("**** Original mismatch columns = " + originalMismatchColumns + "; cleaned mismatch columns = " + cleanedMismatchColumns);
 
         return (originalMismatchColumns == 0 || cleanedMismatchColumns < originalMismatchColumns);
     }
@@ -551,7 +551,7 @@ public class  IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
             }
             difference = indelIndex - newIndex;
         } else if ( ce2.getOperator() == CigarOperator.I ) {
-            int indelIndex = ce1.getLength();
+            int indelIndex = refIndex + ce1.getLength();
             String indelString = readSeq.substring(indelIndex, indelIndex+ce2.getLength());
             int newIndex = indelIndex;
             while ( newIndex > 0 ) {
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/MismatchIntervalWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/MismatchIntervalWalker.java
index 8192643b5..1d5eb2639 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/MismatchIntervalWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/MismatchIntervalWalker.java
@@ -16,7 +16,7 @@ public class MismatchIntervalWalker extends LocusWalker<Pair<GenomeLoc, Boolean>
     @Argument(fullName="windowSize", shortName="window", doc="window size for calculating entropy", required=false)
     public int windowSize = 10;
     @Argument(fullName="mismatchFraction", shortName="mismatch", doc="fraction of mismatching base qualities threshold", required=false)
-    public double mismatchThreshold = 0.20;
+    public double mismatchThreshold = 0.15;
 
     private final int minReadsAtInterval = 4;