diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
index ea28a28e4..8098de5b1 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
@@ -41,7 +41,7 @@ public class DepthOfCoverage extends InfoFieldAnnotation implements StandardAnno
 
         int depth = 0;
         for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() )
-            depth += sample.getValue().getBasePileup().depthOfCoverage();
+            depth += sample.getValue().hasBasePileup() ? sample.getValue().getBasePileup().depthOfCoverage() : sample.getValue().getExtendedEventPileup().depthOfCoverage();
         Map<String, Object> map = new HashMap<String, Object>();
         map.put(getKeyNames().get(0), String.format("%d", depth));
         return map;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
index 7fcb56b1a..ffc852903 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
@@ -43,7 +43,7 @@ public class QualByDepth extends InfoFieldAnnotation implements StandardAnnotati
             if ( context == null )
                 continue;
 
-            depth += context.getBasePileup().depthOfCoverage();
+            depth += context.hasBasePileup() ? context.getBasePileup().depthOfCoverage() : context.getExtendedEventPileup().depthOfCoverage();
         }
 
         if ( depth == 0 )