diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java
index 3f03c2bb2..4cf6586a6 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java
@@ -33,7 +33,9 @@ import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.clipping.ReadClipper;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.pileup.ExtendedEventPileupElement;
+import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
@@ -101,9 +103,21 @@ public class ConsensusAlleleCounter {
         for (Map.Entry<String, AlignmentContext> sample : contexts.entrySet()) {
             AlignmentContext context = AlignmentContextUtils.stratify(sample.getValue(), contextType);
 
-            final ReadBackedExtendedEventPileup indelPileup = context.getExtendedEventPileup();
-            insCount += indelPileup.getNumberOfInsertions();
-            delCount += indelPileup.getNumberOfDeletions();
+            if (context.hasExtendedEventPileup()) {
+                final ReadBackedExtendedEventPileup indelPileup = context.getExtendedEventPileup();
+                insCount += indelPileup.getNumberOfInsertions();
+                delCount += indelPileup.getNumberOfDeletions();
+            }
+            else {
+                // todo - this should be version to be used when extended events are removed
+                // todo - maybe we should create utility functions in ReadBackedPileup definition to do the equivalent thing?
+                for (PileupElement p: context.getBasePileup()) {
+                    if (p.isBeforeDeletion())
+                        delCount++;
+                    else if (p.isBeforeInsertion())
+                        insCount++;
+                }
+            }
         }
 
         if (insCount < minIndelCountForGenotyping && delCount < minIndelCountForGenotyping)
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
index 00d90e3f1..b4b3a94d2 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
@@ -88,7 +88,7 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
         ignoreSNPAllelesWhenGenotypingIndels = UAC.IGNORE_SNP_ALLELES;
     }
 
-    private List<Allele> computeConsensusAlleles(ReferenceContext ref,
+    protected List<Allele> computeConsensusAlleles(ReferenceContext ref,
                                                  Map<String, AlignmentContext> contexts,
                                                  AlignmentContextUtils.ReadOrientation contextType,
                                                  GenomeLocParser locParser) {