diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
index daff48970..cf8712b3a 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
@@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.indels;
 
 import net.sf.samtools.*;
 import net.sf.samtools.util.StringUtil;
+import net.sf.samtools.util.SequenceUtil;
 import net.sf.picard.reference.IndexedFastaSequenceFile;
 import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broadinstitute.sting.commandline.*;
@@ -83,7 +84,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
     @Argument(fullName="maxReadsInRam", shortName="maxInRam", doc="max reads allowed to be kept in memory at a time by the SAMFileWriter. "+
                 "If too low, the tool may run out of system file descriptors needed to perform sorting; if too high, the tool may run out of memory.", required=false)
     protected int MAX_RECORDS_IN_RAM = 500000;
-    
+
     // ADVANCED OPTIONS FOLLOW
 
     @Argument(fullName="maxConsensuses", shortName="maxConsensuses", doc="max alternate consensuses to try (necessary to improve performance in deep coverage)", required=false)
@@ -583,8 +584,14 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
                         // however we don't have enough info to use the proper MAQ scoring system.
                         // For now, we will just arbitrarily add 10 to the mapping quality. [EB, 6/7/2010].
                         // TODO -- we need a better solution here
-                        aRead.getRead().setMappingQuality(Math.min(aRead.getRead().getMappingQuality() + 10, 254));
-                        aRead.getRead().setAttribute("NM", AlignmentUtils.numMismatches(aRead.getRead(), reference, aRead.getRead().getAlignmentStart()-(int)leftmostIndex));
+                        SAMRecord read = aRead.getRead();
+                        read.setMappingQuality(Math.min(aRead.getRead().getMappingQuality() + 10, 254));
+
+                        // fix the attribute tags
+                        if ( read.getAttribute(SAMTag.NM.name()) != null )
+                            read.setAttribute("NM", SequenceUtil.calculateSamNmTag(read, reference, (int)leftmostIndex-1));
+                        if ( read.getAttribute(SAMTag.UQ.name()) != null )
+                            read.setAttribute("UQ", SequenceUtil.sumQualitiesOfMismatches(read, reference, (int)leftmostIndex-1));
                     }
                 }
             }
@@ -1210,25 +1217,10 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
                 if ( newStart != read.getAlignmentStart() )
                     read.setAttribute(ORIGINAL_POSITION_TAG, read.getAlignmentStart());
             }
-            
-            // if it's a paired end read, we need to update the insert size
-            if ( read.getReadPairedFlag() ) {
-                int insertSize = read.getInferredInsertSize();
-                if ( insertSize > 0 ) {
-                    read.setCigar(newCigar);
-                    read.setInferredInsertSize(insertSize + read.getAlignmentStart() - newStart);
-                    read.setAlignmentStart(newStart);
-                } else {
-                    // note that the correct order of actions is crucial here (we can't set the new cigar too early)
-                    int oldEnd = read.getAlignmentEnd();
-                    read.setCigar(newCigar);
-                    read.setAlignmentStart(newStart);
-                    read.setInferredInsertSize(insertSize + oldEnd - read.getAlignmentEnd());
-                }
-            } else {
-                read.setCigar(newCigar);
-                read.setAlignmentStart(newStart);
-            }
+
+            read.setCigar(newCigar);
+            read.setAlignmentStart(newStart);
+
             return true;
         }
 
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
index 69917e147..fba9b4fd3 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
@@ -9,7 +9,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
 
     @Test
     public void testRealignerLod5() {
-        String[] md5s = {"ecff0ce35feb839b6346197db455bbdf", "c4ef635f2597b12b93a73199f07e509b"};
+        String[] md5s = {"2265e03ed1a2290e60208559925c30ef", "c4ef635f2597b12b93a73199f07e509b"};
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T IndelRealigner -noPG -LOD 5 -maxConsensuses 100 -greedy 100 -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10030000 -compress 1 -targetIntervals " + validationDataLocation + "cleaner.test.intervals -o %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe",
                  2,
@@ -19,7 +19,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
 
     @Test
     public void testRealignerLod50() {
-        String[] md5s = {"ecff0ce35feb839b6346197db455bbdf", "3735a510513b6fa4161d92155e026283"};
+        String[] md5s = {"2265e03ed1a2290e60208559925c30ef", "3735a510513b6fa4161d92155e026283"};
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T IndelRealigner -noPG -LOD 50 -maxConsensuses 100 -greedy 100 -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10030000 -compress 1 -targetIntervals " + validationDataLocation + "cleaner.test.intervals -o %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe",
                  2,
@@ -29,7 +29,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
 
     @Test
     public void testRealignerKnownsOnly() {
-        String[] md5s = {"70b657dcb654bd2c84c38d654c5af697", "74652bd8240291293ec921f8ecfa1622"};
+        String[] md5s = {"dc2fe2856840b12a34bb57de2ca71cd0", "74652bd8240291293ec921f8ecfa1622"};
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T IndelRealigner -noPG -LOD 1.0 -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10076000 -compress 1 -targetIntervals " + validationDataLocation + "NA12878.indels.intervals -B:knownIndels,VCF " + validationDataLocation + "NA12878.indels.vcf4 -o %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe -knownsOnly",
                  2,