diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelConsistencyReadCounter.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelConsistencyReadCounter.java
index 66c150ca0..abff66830 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelConsistencyReadCounter.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelConsistencyReadCounter.java
@@ -97,6 +97,10 @@ public class IndelConsistencyReadCounter extends ReadWalker<Integer, Integer> {
     private static boolean containsIndel(final SAMRecord r, final VariantContext vc) {
         int indelStart = vc.getStart() + 1;
         int readPos = r.getAlignmentStart();
+
+        if ( vc.isInsertion() && indelStart == readPos )
+            return true;
+
         final Cigar cigar = r.getCigar();
 
         int idx = 0;
@@ -106,7 +110,6 @@ public class IndelConsistencyReadCounter extends ReadWalker<Integer, Integer> {
             switch ( ce.getOperator() ) {
                 case M:
                 case I:
-                case S:
                     readPos += ce.getLength();
                     break;
                 default:
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/RealignedReadCounter.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/RealignedReadCounter.java
index e6688c691..03777e8ec 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/RealignedReadCounter.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/RealignedReadCounter.java
@@ -109,7 +109,9 @@ public class RealignedReadCounter extends ReadWalker<Integer, Integer> {
 
     private int getIndelSize(SAMRecord read) {
         for ( CigarElement ce : read.getCigar().getCigarElements() ) {
-            if ( ce.getOperator() == CigarOperator.I || ce.getOperator() == CigarOperator.D )
+            if ( ce.getOperator() == CigarOperator.I )
+                return 0;
+            if ( ce.getOperator() == CigarOperator.D )
                 return ce.getLength();
         }
         logger.warn("We didn't see an indel for this read: " + read.getReadName() + " " + read.getAlignmentStart() + " " + read.getCigar());