diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java b/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
index 75af7976f..64f914064 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
@@ -318,6 +318,7 @@ public class LocusIteratorByState extends LocusIterator {
                         continue;
 
                     if (op == CigarOperator.D) {
+                        // TODO -- LIBS is totally busted for deletions so that reads with Ds right before Is in their CIGAR are broken; must fix
                         if (readInfo.includeReadsWithDeletionAtLoci()) {            // only add deletions to the pileup if we are authorized to do so
                             pile.add(new PileupElement(read, readOffset, true, isBeforeDeletion, isAfterDeletion, isBeforeInsertion, isAfterInsertion, isNextToSoftClip, null, nextOp == CigarOperator.D ? nextElementLength : -1));
                             size++;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
index 5d83ddd51..61e30f3b9 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
@@ -88,7 +88,11 @@ public class DepthPerAlleleBySample extends GenotypeAnnotation implements Standa
         for ( PileupElement p : pileup ) {
             if ( p.isBeforeInsertion() ) {
 
-                final Allele insertion = Allele.create((char)refBase + p.getEventBases(), false);
+                final String eventBases = p.getEventBases();
+                if ( eventBases == null )
+                    continue;
+
+                final Allele insertion = Allele.create((char)refBase + eventBases, false);
                 if ( alleleCounts.containsKey(insertion) ) {
                     alleleCounts.put(insertion, alleleCounts.get(insertion)+1);
                 }