diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java b/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
index 2257cc139..703308da3 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
@@ -472,13 +472,13 @@ public class LocusIteratorByState extends LocusIterator {
                         if (op == CigarOperator.D) {
                             if (readInfo.includeReadsWithDeletionAtLoci()) {          // only add deletions to the pileup if we are authorized to do so
                                 int leftAlignedStart = (eventStartOffset < 0) ? readOffset : eventStartOffset;
-                                pile.add(new PileupElement(read, leftAlignedStart, true, nextOp == CigarOperator.I, false));
+                                pile.add(new PileupElement(read, leftAlignedStart, true, nextOp == CigarOperator.I, nextOp == CigarOperator.S || (state.getGenomeOffset() == 0 && read.getSoftStart() != read.getAlignmentStart())));
                                 size++;
                                 nDeletions++;
                             }
                         } else {
                             if (!filterBaseInRead(read, location.getStart())) {
-                                pile.add(new PileupElement(read, readOffset, false, nextOp == CigarOperator.I, op == CigarOperator.S));
+                                pile.add(new PileupElement(read, readOffset, false, nextOp == CigarOperator.I, nextOp == CigarOperator.S || (state.getGenomeOffset() == 0 && read.getSoftStart() != read.getAlignmentStart())));
                                 size++;
                             }
                         }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
index 5980ff356..ea53c815d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
@@ -212,7 +212,7 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
 
     public class BAQedPileupElement extends PileupElement {
         public BAQedPileupElement( final PileupElement PE ) {
-            super(PE.getRead(), PE.getOffset(), PE.isDeletion(), PE.isBeforeInsertion(), PE.isSoftClipped());
+            super(PE.getRead(), PE.getOffset(), PE.isDeletion(), PE.isBeforeInsertion(), PE.isNextToSoftClip());
         }
 
         @Override
diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java b/public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java
index f4fa9e941..82e403842 100644
--- a/public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java
+++ b/public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java
@@ -204,7 +204,7 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
 
     protected abstract AbstractReadBackedPileup<RBP, PE> createNewPileup(GenomeLoc loc, PileupElementTracker<PE> pileupElementTracker);
 
-    protected abstract PE createNewPileupElement(GATKSAMRecord read, int offset, boolean isDeletion, boolean isBeforeInsertion, boolean isSoftClipped);
+    protected abstract PE createNewPileupElement(GATKSAMRecord read, int offset, boolean isDeletion, boolean isBeforeInsertion, boolean isNextToSoftClip);
 
     // --------------------------------------------------------
     //
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 87aa31c47..d67261ba2 100755
--- a/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java
+++ b/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java
@@ -24,7 +24,7 @@ public class PileupElement implements Comparable<PileupElement> {
     protected final int offset;
     protected final boolean isDeletion;
     protected final boolean isBeforeInsertion;
-    protected final boolean isSoftClipped;
+    protected final boolean isNextToSoftClip;
 
 
     /**
@@ -34,13 +34,13 @@ public class PileupElement implements Comparable<PileupElement> {
      * @param offset            the position in the read for this base. All deletions must be left aligned! (-1 is only allowed for reads starting with insertions)
      * @param isDeletion        whether or not this base is a deletion
      * @param isBeforeInsertion whether or not this base is before an insertion
-     * @param isSoftClipped     whether or not this base was softclipped
+     * @param isNextToSoftClip  whether or not this base is next to a soft clipped base
      */
     @Requires({
             "read != null",
             "offset >= -1",
             "offset <= read.getReadLength()"})
-    public PileupElement(final GATKSAMRecord read, final int offset, final boolean isDeletion, final boolean isBeforeInsertion, final boolean isSoftClipped) {
+    public PileupElement(final GATKSAMRecord read, final int offset, final boolean isDeletion, final boolean isBeforeInsertion, final boolean isNextToSoftClip) {
         if (offset < 0 && isDeletion)
             throw new ReviewedStingException("Pileup Element cannot create a deletion with a negative offset");
 
@@ -48,7 +48,7 @@ public class PileupElement implements Comparable<PileupElement> {
         this.offset = offset;
         this.isDeletion = isDeletion;
         this.isBeforeInsertion = isBeforeInsertion;
-        this.isSoftClipped = isSoftClipped;
+        this.isNextToSoftClip = isNextToSoftClip;
     }
 
     public boolean isDeletion() {
@@ -59,8 +59,8 @@ public class PileupElement implements Comparable<PileupElement> {
         return isBeforeInsertion;
     }
 
-    public boolean isSoftClipped() {
-        return isSoftClipped;
+    public boolean isNextToSoftClip() {
+        return isNextToSoftClip;
     }
 
     public boolean isInsertionAtBeginningOfRead() {
diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java b/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java
index 641c63f6c..df334f557 100644
--- a/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java
+++ b/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java
@@ -96,7 +96,7 @@ public class ReadBackedExtendedEventPileupImpl extends AbstractReadBackedPileup<
     }
 
     @Override
-    protected ExtendedEventPileupElement createNewPileupElement(GATKSAMRecord read, int offset, boolean isDeletion, boolean isBeforeInsertion, boolean isSoftClipped) {
+    protected ExtendedEventPileupElement createNewPileupElement(GATKSAMRecord read, int offset, boolean isDeletion, boolean isBeforeInsertion, boolean isNextToSoftClip) {
         throw new UnsupportedOperationException("Not enough information provided to create a new pileup element");
     }
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileupImpl.java b/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileupImpl.java
index 965e74e8b..20b100001 100644
--- a/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileupImpl.java
+++ b/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileupImpl.java
@@ -71,7 +71,7 @@ public class ReadBackedPileupImpl extends AbstractReadBackedPileup<ReadBackedPil
     }
 
     @Override
-    protected PileupElement createNewPileupElement(GATKSAMRecord read, int offset, boolean isDeletion, boolean isBeforeInsertion, boolean isSoftClipped) {
-        return new PileupElement(read, offset, isDeletion, isBeforeInsertion, isSoftClipped);
+    protected PileupElement createNewPileupElement(GATKSAMRecord read, int offset, boolean isDeletion, boolean isBeforeInsertion, boolean isNextToSoftClip) {
+        return new PileupElement(read, offset, isDeletion, isBeforeInsertion, isNextToSoftClip);
     }
 }