diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java
index 746d4cbbd..8f396c7b4 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java
@@ -246,7 +246,7 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Set<Bas
         }
 
         for ( int prevBase = 1; prevBase <= nPreviousBases; prevBase ++ ) {
-            if ( Character.toUpperCase(read.getReadBases()[offset + prevBase*c]) != Character.toUpperCase(ref.getBases()[nPreviousBases+1+prevBase*c]) ) {
+            if ( Character.toUpperCase(read.getReadBases()[offset + prevBase*c]) != Character.toUpperCase(ref.getBases()[nPreviousBases+1+prevBase*c]) || ! BaseUtils.isRegularBase(ref.getBases()[nPreviousBases+1+prevBase*c])) {
                 return true;
             }
         }
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/IndelCounterWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/IndelCounterWalker.java
new file mode 100755
index 000000000..716600d7c
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/IndelCounterWalker.java
@@ -0,0 +1,52 @@
+package org.broadinstitute.sting.playground.gatk.walkers;
+
+import org.broadinstitute.sting.gatk.walkers.LocusWalker;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.utils.ReadBackedPileup;
+import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.BasicPileup;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: chartl
+ * Date: Oct 28, 2009
+ * Time: 3:19:48 PM
+ * To change this template use File | Settings | File Templates.
+ */
+public class IndelCounterWalker extends LocusWalker<Integer,Integer> {
+
+    public Integer reduceInit() {
+        return 0;
+    }
+
+    public Integer reduce( Integer prevReduce, Integer map ) {
+        return map + prevReduce;
+    }
+
+    public Integer treeReduce( Integer reduce1, Integer reduce2 ) {
+        return reduce(reduce1,reduce2);
+    }
+
+    public Integer map ( RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context ) {
+        if (BaseUtils.isRegularBase(ref.getBase()) ) {
+            return numIndels(context);
+        } else {
+            return 0;
+        }
+    }
+
+    public Integer numIndels ( AlignmentContext context ) {
+        String[] indelPileup = BasicPileup.indelPileup(context.getReads(),context.getOffsets());
+        // number of indels is the number of non-"null" indeces
+        int nIndel = 0;
+        for( String indel : indelPileup ) {
+            if ( ! indel.equals("null") ) {  // currently how non-indel bases are represented in pileup
+                nIndel ++;
+            }
+        }
+
+        return nIndel;
+    }
+}