diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/AdvancedRecalibrationEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/AdvancedRecalibrationEngine.java
index e5c952b76..ff1754a10 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/AdvancedRecalibrationEngine.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/AdvancedRecalibrationEngine.java
@@ -106,47 +106,49 @@ public class AdvancedRecalibrationEngine extends StandardRecalibrationEngine imp
     }
 
     @Override
-    public synchronized void updateDataForRead(final GATKSAMRecord read, final double[] snpErrors, final double[] insertionErrors, final double[] deletionErrors ) {
+    public synchronized void updateDataForRead(final GATKSAMRecord read, final boolean[] skip, final double[] snpErrors, final double[] insertionErrors, final double[] deletionErrors ) {
         for( int offset = 0; offset < read.getReadBases().length; offset++ ) {
-            final ReadCovariates readCovariates = covariateKeySetFrom(read);
+            if( !skip[offset] ) {
+                final ReadCovariates readCovariates = covariateKeySetFrom(read);
 
-            tempQualArray[EventType.BASE_SUBSTITUTION.index] = read.getBaseQualities()[offset];
-            tempFractionalErrorArray[EventType.BASE_SUBSTITUTION.index] = snpErrors[offset];
-            tempQualArray[EventType.BASE_INSERTION.index] = read.getBaseInsertionQualities()[offset];
-            tempFractionalErrorArray[EventType.BASE_INSERTION.index] = insertionErrors[offset];
-            tempQualArray[EventType.BASE_DELETION.index] = read.getBaseDeletionQualities()[offset];
-            tempFractionalErrorArray[EventType.BASE_DELETION.index] = deletionErrors[offset];
+                tempQualArray[EventType.BASE_SUBSTITUTION.index] = read.getBaseQualities()[offset];
+                tempFractionalErrorArray[EventType.BASE_SUBSTITUTION.index] = snpErrors[offset];
+                tempQualArray[EventType.BASE_INSERTION.index] = read.getBaseInsertionQualities()[offset];
+                tempFractionalErrorArray[EventType.BASE_INSERTION.index] = insertionErrors[offset];
+                tempQualArray[EventType.BASE_DELETION.index] = read.getBaseDeletionQualities()[offset];
+                tempFractionalErrorArray[EventType.BASE_DELETION.index] = deletionErrors[offset];
 
-            for (final EventType eventType : EventType.values()) {
-                final int[] keys = readCovariates.getKeySet(offset, eventType);
-                final int eventIndex = eventType.index;
-                final byte qual = tempQualArray[eventIndex];
-                final double isError = tempFractionalErrorArray[eventIndex];
+                for (final EventType eventType : EventType.values()) {
+                    final int[] keys = readCovariates.getKeySet(offset, eventType);
+                    final int eventIndex = eventType.index;
+                    final byte qual = tempQualArray[eventIndex];
+                    final double isError = tempFractionalErrorArray[eventIndex];
 
-                final NestedIntegerArray<RecalDatum> rgRecalTable = recalibrationTables.getTable(RecalibrationTables.TableType.READ_GROUP_TABLE);
-                final RecalDatum rgPreviousDatum = rgRecalTable.get(keys[0], eventIndex);
-                final RecalDatum rgThisDatum = createDatumObject(qual, isError);
-                if (rgPreviousDatum == null) // key doesn't exist yet in the map so make a new bucket and add it
-                    rgRecalTable.put(rgThisDatum, keys[0], eventIndex);
-                else
-                    rgPreviousDatum.combine(rgThisDatum);
-
-                final NestedIntegerArray<RecalDatum> qualRecalTable = recalibrationTables.getTable(RecalibrationTables.TableType.QUALITY_SCORE_TABLE);
-                final RecalDatum qualPreviousDatum = qualRecalTable.get(keys[0], keys[1], eventIndex);
-                if (qualPreviousDatum == null)
-                    qualRecalTable.put(createDatumObject(qual, isError), keys[0], keys[1], eventIndex);
-                else
-                    qualPreviousDatum.increment(1.0, isError);
-
-                for (int i = 2; i < covariates.length; i++) {
-                    if (keys[i] < 0)
-                        continue;
-                    final NestedIntegerArray<RecalDatum> covRecalTable = recalibrationTables.getTable(i);
-                    final RecalDatum covPreviousDatum = covRecalTable.get(keys[0], keys[1], keys[i], eventIndex);
-                    if (covPreviousDatum == null)
-                        covRecalTable.put(createDatumObject(qual, isError), keys[0], keys[1], keys[i], eventIndex);
+                    final NestedIntegerArray<RecalDatum> rgRecalTable = recalibrationTables.getTable(RecalibrationTables.TableType.READ_GROUP_TABLE);
+                    final RecalDatum rgPreviousDatum = rgRecalTable.get(keys[0], eventIndex);
+                    final RecalDatum rgThisDatum = createDatumObject(qual, isError);
+                    if (rgPreviousDatum == null) // key doesn't exist yet in the map so make a new bucket and add it
+                        rgRecalTable.put(rgThisDatum, keys[0], eventIndex);
                     else
-                        covPreviousDatum.increment(1.0, isError);
+                        rgPreviousDatum.combine(rgThisDatum);
+
+                    final NestedIntegerArray<RecalDatum> qualRecalTable = recalibrationTables.getTable(RecalibrationTables.TableType.QUALITY_SCORE_TABLE);
+                    final RecalDatum qualPreviousDatum = qualRecalTable.get(keys[0], keys[1], eventIndex);
+                    if (qualPreviousDatum == null)
+                        qualRecalTable.put(createDatumObject(qual, isError), keys[0], keys[1], eventIndex);
+                    else
+                        qualPreviousDatum.increment(1.0, isError);
+
+                    for (int i = 2; i < covariates.length; i++) {
+                        if (keys[i] < 0)
+                            continue;
+                        final NestedIntegerArray<RecalDatum> covRecalTable = recalibrationTables.getTable(i);
+                        final RecalDatum covPreviousDatum = covRecalTable.get(keys[0], keys[1], keys[i], eventIndex);
+                        if (covPreviousDatum == null)
+                            covRecalTable.put(createDatumObject(qual, isError), keys[0], keys[1], keys[i], eventIndex);
+                        else
+                            covPreviousDatum.increment(1.0, isError);
+                    }
                 }
             }
         }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationEngine.java
index ab65c1462..ce60f5a3a 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationEngine.java
@@ -35,5 +35,5 @@ public interface RecalibrationEngine {
 
     public void updateDataForPileupElement(final PileupElement pileupElement, final byte refBase);
 
-    public void updateDataForRead(final GATKSAMRecord read, final double[] snpErrors, final double[] insertionErrors, final double[] deletionErrors);
+    public void updateDataForRead(final GATKSAMRecord read, final boolean[] skip, final double[] snpErrors, final double[] insertionErrors, final double[] deletionErrors);
 }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java
index 76a82a134..2b0f8ca80 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java
@@ -93,7 +93,7 @@ public class StandardRecalibrationEngine implements RecalibrationEngine, PublicP
     }
 
     @Override
-    public synchronized void updateDataForRead( final GATKSAMRecord read, final double[] snpErrors, final double[] insertionErrors, final double[] deletionErrors ) {
+    public synchronized void updateDataForRead( final GATKSAMRecord read, final boolean[] skip, final double[] snpErrors, final double[] insertionErrors, final double[] deletionErrors ) {
         throw new UnsupportedOperationException("Delocalized BQSR is not available in the GATK-lite version");
     }