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 92e6f8536..40bf6bbd8 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
@@ -56,12 +56,12 @@ 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 );
+                final int offset = ReadUtils.getReadCoordinateForReferenceCoordinate( read.getSoftStart(), 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 );
+                final int numAlignedBases = AlignmentUtils.getNumAlignedBasesCountingSoftClips( read );
                 if (readPos > numAlignedBases / 2)
                     readPos = numAlignedBases - (readPos + 1);
 
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 998045a8b..cecbd1bc4 100644
--- a/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
@@ -342,6 +342,18 @@ public class AlignmentUtils {
         return n;
     }
 
+    public static int getNumAlignedBasesCountingSoftClips(final SAMRecord r) {
+        int n = 0;
+        final Cigar cigar = r.getCigar();
+        if (cigar == null) return 0;
+
+        for (final CigarElement e : cigar.getCigarElements())
+            if (e.getOperator() == CigarOperator.M || e.getOperator() == CigarOperator.S)
+                n += e.getLength();
+
+        return n;
+    }
+
     public static byte[] alignmentToByteArray(final Cigar cigar, final byte[] read, final byte[] ref) {
 
         final byte[] alignment = new byte[read.length];