diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
index 6eea12e2b..526f25797 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
@@ -30,7 +30,7 @@ public class BaseQualityRankSumTest extends RankSumTest {
             }
         }
     }
-    protected void fillQualsFromPileup(final Allele ref, final List<Allele> alts, final Map<Allele, List<GATKSAMRecord>> stratifiedContext, final List<Double> refQuals, List<Double> altQuals) {
+    protected void fillQualsFromPileup(final Allele ref, final List<Allele> alts, final int refLoc, final Map<Allele, List<GATKSAMRecord>> stratifiedContext, final List<Double> refQuals, final List<Double> altQuals) {
         // TODO -- implement me; how do we pull out the correct offset from the read?
         return;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
index 520b0f232..749278ce7 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
@@ -34,7 +34,7 @@ public class MappingQualityRankSumTest extends RankSumTest {
         }
     }
 
-    protected void fillQualsFromPileup(final Allele ref, final List<Allele> alts, final Map<Allele, List<GATKSAMRecord>> stratifiedContext, final List<Double> refQuals, List<Double> altQuals) {
+    protected void fillQualsFromPileup(final Allele ref, final List<Allele> alts, final int refLoc, final Map<Allele, List<GATKSAMRecord>> stratifiedContext, final List<Double> refQuals, final List<Double> altQuals) {
         for ( final Map.Entry<Allele, List<GATKSAMRecord>> alleleBin : stratifiedContext.entrySet() ) {
             final boolean matchesRef = ref.equals(alleleBin.getKey());
             final boolean matchesAlt = alts.contains(alleleBin.getKey());
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
index 80d248ac2..ad9600edf 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
@@ -123,7 +123,7 @@ public abstract class RankSumTest extends InfoFieldAnnotation implements Standar
             if ( context == null )
                 continue;
 
-            fillQualsFromPileup(vc.getReference(), vc.getAlternateAlleles(), context, refQuals, altQuals);
+            fillQualsFromPileup(vc.getReference(), vc.getAlternateAlleles(), vc.getStart(), context, refQuals, altQuals);
         }
 
         if ( refQuals.size() == 0 || altQuals.size() == 0 )
@@ -146,7 +146,7 @@ public abstract class RankSumTest extends InfoFieldAnnotation implements Standar
         return map;
     }
 
-    protected abstract void fillQualsFromPileup(final Allele ref, final List<Allele> alts, final Map<Allele, List<GATKSAMRecord>> stratifiedContext, final List<Double> refQuals, List<Double> altQuals);
+    protected abstract void fillQualsFromPileup(final Allele ref, final List<Allele> alts, final int refLoc, final Map<Allele, List<GATKSAMRecord>> stratifiedContext, final List<Double> refQuals, List<Double> altQuals);
 
     protected abstract void fillQualsFromPileup(final byte ref, final List<Byte> alts, final ReadBackedPileup pileup, final List<Double> refQuals, final List<Double> altQuals);
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
index e013f0e08..9ff8886cf 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
@@ -12,6 +12,7 @@ import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.sam.AlignmentUtils;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.sting.utils.sam.ReadUtils;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 
 import java.util.*;
@@ -47,11 +48,7 @@ public class ReadPosRankSumTest extends RankSumTest {
         }
     }
 
-    protected void fillQualsFromPileup(final Allele ref, final List<Allele> alts, final Map<Allele, List<GATKSAMRecord>> stratifiedContext, final List<Double> refQuals, List<Double> altQuals) {
-        // TODO -- implement me; how do we pull out the correct offset from the read?
-        return;
-
-/*
+    protected void fillQualsFromPileup(final Allele ref, final List<Allele> alts, final int refLoc, final Map<Allele, List<GATKSAMRecord>> stratifiedContext, final List<Double> refQuals, final List<Double> altQuals) {
         for ( final Map.Entry<Allele, List<GATKSAMRecord>> alleleBin : stratifiedContext.entrySet() ) {
             final boolean matchesRef = ref.equals(alleleBin.getKey());
             final boolean matchesAlt = alts.contains(alleleBin.getKey());
@@ -59,13 +56,21 @@ public class ReadPosRankSumTest extends RankSumTest {
                 continue;
 
             for ( final GATKSAMRecord read : alleleBin.getValue() ) {
+                final int offset = ReadUtils.getReadCoordinateForReferenceCoordinate( read.getUnclippedStart(), read.getCigar(), refLoc, ReadUtils.ClippingTail.RIGHT_TAIL, true );
+                if ( offset == ReadUtils.CLIPPING_GOAL_NOT_REACHED )
+                    continue;
+                int readPos = AlignmentUtils.calcAlignmentByteArrayOffset( read.getCigar(), offset, false, false, 0, 0 );
+
+                final int numAlignedBases = AlignmentUtils.getNumAlignedBases( read );
+                if (readPos > numAlignedBases / 2)
+                    readPos = numAlignedBases - (readPos + 1);
+
                 if ( matchesRef )
-                    refQuals.add((double)read.getMappingQuality());
+                    refQuals.add((double) readPos);
                 else
-                    altQuals.add((double)read.getMappingQuality());
+                    altQuals.add((double) readPos);
             }
         }
-*/
     }
 
     protected void fillIndelQualsFromPileup(ReadBackedPileup pileup, List<Double> refQuals, List<Double> altQuals) {
diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java b/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java
index 81ba00888..e5cd9f4d5 100755
--- a/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java
+++ b/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java
@@ -73,7 +73,7 @@ public class PileupElement implements Comparable<PileupElement> {
     }
 
     public PileupElement(final GATKSAMRecord read, final int offset, final boolean isDeletion, final boolean isBeforeDeletion, final boolean isAfterDeletion, final boolean isBeforeInsertion, final boolean isAfterInsertion, final boolean isNextToSoftClip) {
-        this(read,offset, isDeletion, isBeforeDeletion, isAfterDeletion, isBeforeInsertion, isAfterInsertion, isNextToSoftClip, null, -1);
+        this(read, offset, isDeletion, isBeforeDeletion, isAfterDeletion, isBeforeInsertion, isAfterInsertion, isNextToSoftClip, null, -1);
     }
     public boolean isDeletion() {
         return isDeletion;
diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java b/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
index 3b2736418..e0fee66ef 100644
--- a/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
@@ -381,15 +381,19 @@ public class AlignmentUtils {
         return alignment;
     }
 
-    public static int calcAlignmentByteArrayOffset(final Cigar cigar, PileupElement pileup, final int alignmentStart, final int refLocus) {
-        int pileupOffset = pileup.getOffset();
+    public static int calcAlignmentByteArrayOffset(final Cigar cigar, final PileupElement pileupElement, final int alignmentStart, final int refLocus) {
+        return calcAlignmentByteArrayOffset( cigar, pileupElement.getOffset(), pileupElement.isInsertionAtBeginningOfRead(), pileupElement.isDeletion(), alignmentStart, refLocus );
+    }
+
+    public static int calcAlignmentByteArrayOffset(final Cigar cigar, final int offset, final boolean isInsertionAtBeginningOfRead, final boolean isDeletion, final int alignmentStart, final int refLocus) {
+        int pileupOffset = offset;
 
         // Special case for reads starting with insertion
-        if (pileup.isInsertionAtBeginningOfRead())
+        if (isInsertionAtBeginningOfRead)
             return 0;
 
         // Reassign the offset if we are in the middle of a deletion because of the modified representation of the read bases
-        if (pileup.isDeletion()) {
+        if (isDeletion) {
             pileupOffset = refLocus - alignmentStart;
             final CigarElement ce = cigar.getCigarElement(0);
             if (ce.getOperator() == CigarOperator.S) {
@@ -414,7 +418,7 @@ public class AlignmentUtils {
                     break;
                 case D:
                 case N:
-                    if (!pileup.isDeletion()) {
+                    if (!isDeletion) {
                         alignmentPos += elementLength;
                     } else {
                         if (pos + elementLength - 1 >= pileupOffset) {