diff --git a/java/src/org/broadinstitute/sting/gatk/contexts/StratifiedAlignmentContext.java b/java/src/org/broadinstitute/sting/gatk/contexts/StratifiedAlignmentContext.java
index 7d2882dbb..4b0ac4b19 100755
--- a/java/src/org/broadinstitute/sting/gatk/contexts/StratifiedAlignmentContext.java
+++ b/java/src/org/broadinstitute/sting/gatk/contexts/StratifiedAlignmentContext.java
@@ -39,6 +39,7 @@ import java.util.Map;
 /**
  * Useful class for storing different AlignmentContexts
  * User: ebanks
+ * Modified: chartl (split by read group)
  */
 public class StratifiedAlignmentContext {
 
@@ -140,6 +141,40 @@ public class StratifiedAlignmentContext {
             myContext.add(read, p.getOffset());
         }
 
+        return contexts;
+    }
+
+     /**
+     * Splits the given AlignmentContext into a StratifiedAlignmentContext per read group.
+     *
+     * @param pileup                the original pileup
+     * @return a Map of sample name to StratifiedAlignmentContext
+     * @todo - support for collapsing or assuming read groups if they are missing
+     *
+     **/
+    public static Map<String,StratifiedAlignmentContext> splitContextByReadGroup(ReadBackedPileup pileup) {
+        HashMap<String,StratifiedAlignmentContext> contexts = new HashMap<String,StratifiedAlignmentContext>();
+
+        for ( PileupElement p : pileup ) {
+            SAMRecord read = p.getRead();
+
+            SAMReadGroupRecord readGroup = read.getReadGroup();
+            if ( readGroup == null ) {
+                throw new StingException("Missing read group for read " + read.getReadName());
+            }
+
+            String group = readGroup.getReadGroupId();
+
+            StratifiedAlignmentContext myContext = contexts.get(group);
+
+            if ( myContext == null ) {
+                myContext = new StratifiedAlignmentContext(pileup.getLocation());
+                contexts.put(group,myContext);
+            }
+
+            myContext.add(read,p.getOffset());
+        }
+
         return contexts;
     }
 }
\ No newline at end of file
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/coverage/CoverageStatistics.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/coverage/CoverageStatistics.java
index 9a4a96d2e..6340a4f25 100644
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/coverage/CoverageStatistics.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/coverage/CoverageStatistics.java
@@ -141,12 +141,17 @@ public class CoverageStatistics extends LocusWalker<Map<String,Integer>, DepthOf
     }
 
     public Map<String,Integer> map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
-        Map<String, StratifiedAlignmentContext> contextsBySample =
-                                            StratifiedAlignmentContext.splitContextBySample(context.getBasePileup());
+        Map<String,StratifiedAlignmentContext> contexts;
+        if ( useReadGroup ) {
+            contexts = StratifiedAlignmentContext.splitContextByReadGroup(context.getBasePileup());
+        } else {
+            contexts = StratifiedAlignmentContext.splitContextBySample(context.getBasePileup());
+        }
+
         HashMap<String,Integer> depthBySample = new HashMap<String,Integer>();
 
-        for ( String sample : contextsBySample.keySet() ) {
-            AlignmentContext sampleContext = contextsBySample.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE);
+        for ( String sample : contexts.keySet() ) {
+            AlignmentContext sampleContext = contexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE);
             int properDepth = 0;
             for ( PileupElement e : sampleContext.getBasePileup() ) {
                 if ( e.getQual() >= minBaseQuality && e.getMappingQual() >= minMappingQuality ) {