diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
index 2a5ebf027..37ede7f2c 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
@@ -43,6 +43,7 @@ import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broad.tribble.util.variantcontext.Allele;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
 
 import java.util.*;
@@ -130,7 +131,7 @@ private HaplotypeIndelErrorModel model;
 
             for ( ExtendedEventPileupElement p : indelPileup.toExtendedIterable() ) {
                 //SAMRecord read = p.getRead();
-                 SAMRecord read = ReadUtils.hardClipAdaptorSequence(p.getRead());
+                 GATKSAMRecord read = ReadUtils.hardClipAdaptorSequence(p.getRead());
                 if (read == null)
                     continue;     
                 if(ReadUtils.is454Read(read)) {
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
index 4e328ded3..e84a05a7d 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
@@ -751,7 +751,7 @@ public class PairHMMIndelErrorModel {
             }
         }
         for (SAMRecord pread : pileup.getReads()) {
-            SAMRecord read = ReadUtils.hardClipAdaptorSequence(pread);
+            GATKSAMRecord read = ReadUtils.hardClipAdaptorSequence(pread);
             if (read == null)
                 continue;
 
@@ -781,7 +781,7 @@ public class PairHMMIndelErrorModel {
                         qualityScoreByFullCovariateKey.put(qualityScore, fullCovariateKey);
                     }
 
-                    recalQuals[offset] = (double)qualityScore;
+                    recalQuals[offset] = -((double)qualityScore)/10.0;
                 }
 
                 // for each read/haplotype combination, compute likelihoods, ie -10*log10(Pr(R | Hi))
diff --git a/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java b/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
index 02a1bdb5d..e30584113 100644
--- a/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
@@ -182,10 +182,10 @@ public class ReadUtils {
      * @param adaptorLength  length of adaptor sequence
      * @return a new read with adaptor sequence hard-clipped out or null if read is fully clipped
      */
-    public static SAMRecord hardClipAdaptorSequence(final SAMRecord rec, int adaptorLength) {
+    public static GATKSAMRecord hardClipAdaptorSequence(final SAMRecord rec, int adaptorLength) {
 
         Pair<Integer, Integer> adaptorBoundaries = getAdaptorBoundaries(rec, adaptorLength);
-        SAMRecord result = rec;
+        GATKSAMRecord result = (GATKSAMRecord)rec;
 
         if ( adaptorBoundaries != null ) {
             if ( rec.getReadNegativeStrandFlag() && adaptorBoundaries.second >= rec.getAlignmentStart() && adaptorBoundaries.first < rec.getAlignmentEnd() )
@@ -198,7 +198,7 @@ public class ReadUtils {
     }
 
     // return true if the read needs to be completely clipped
-    private static SAMRecord hardClipStartOfRead(SAMRecord oldRec, int stopPosition) {
+    private static GATKSAMRecord hardClipStartOfRead(SAMRecord oldRec, int stopPosition) {
 
         if ( stopPosition >= oldRec.getAlignmentEnd() ) {
             // BAM representation issue -- we can't clip away all bases in a read, just leave it alone and let the filter deal with it
@@ -206,9 +206,9 @@ public class ReadUtils {
             return null;
         }
 
-        SAMRecord rec;
+        GATKSAMRecord rec;
         try {
-            rec = (SAMRecord)oldRec.clone();
+            rec = (GATKSAMRecord)oldRec.clone();
         } catch (Exception e) {
             return null;
         }
@@ -278,7 +278,7 @@ public class ReadUtils {
         return rec;
     }
 
-    private static SAMRecord hardClipEndOfRead(SAMRecord oldRec, int startPosition) {
+    private static GATKSAMRecord hardClipEndOfRead(SAMRecord oldRec, int startPosition) {
 
         if ( startPosition <= oldRec.getAlignmentStart() ) {
             // BAM representation issue -- we can't clip away all bases in a read, just leave it alone and let the filter deal with it
@@ -286,9 +286,9 @@ public class ReadUtils {
             return null;
         }
 
-        SAMRecord rec;
+        GATKSAMRecord rec;
         try {
-            rec = (SAMRecord)oldRec.clone();
+            rec = (GATKSAMRecord)oldRec.clone();
         } catch (Exception e) {
             return null;
         }
@@ -430,7 +430,7 @@ public class ReadUtils {
      * @param rec  original SAM record
      * @return a new read with adaptor sequence hard-clipped out or null if read is fully clipped
      */
-    public static SAMRecord hardClipAdaptorSequence(final SAMRecord rec) {
+    public static GATKSAMRecord hardClipAdaptorSequence(final SAMRecord rec) {
         return hardClipAdaptorSequence(rec, DEFAULT_ADAPTOR_SIZE);
     }
 
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
index 49c2459d8..773c1bca9 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
@@ -34,7 +34,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
 
     @Test
     public void testMultiSamplePilot2AndRecallingWithAlleles() {
-        String md5 = "87a99063152ca935a1bec87ef19e0dad";
+        String md5 = "93d2571e686740c5c775b1fb862b62ec";
 
         WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
                 baseCommand + " -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,050,000", 1,
@@ -248,7 +248,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                         " -o %s" +
                         " -L 1:10,000,000-10,500,000",
                 1,
-                Arrays.asList("84bc209f38d60f325f1a8b6292a82c82"));
+                Arrays.asList("3a6ba2d9b9a5c606389d3353bb27bbe8"));
 
         executeTest(String.format("test indel caller in SLX"), spec);
     }
@@ -276,7 +276,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                          " -o %s" +
                          " -L 1:10,000,000-10,500,000",
                  1,
-                 Arrays.asList("e9b4fef2cdfa4c4657f0df53309131b6"));
+                 Arrays.asList("592a214b8ca1b62733f9627adb631f16"));
 
          executeTest(String.format("test indel calling, multiple technologies"), spec);
      }