diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java
index d554061c8..8b342dcd7 100644
--- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java
+++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java
@@ -303,7 +303,12 @@ public class ConstrainedMateFixingManager {
                     }
 
                     // we've already seen our mate -- set the mate info and remove it from the map
-                    SamPairUtil.setMateInfo(mate.record, newRead, null);
+                    // Via Nils Homer:
+                    //   There will be two SamPairUtil.setMateInfo functions.  The default will not update the mate
+                    //   cigar tag; in fact, it will remove it if it is present.  An alternative SamPairUtil.setMateInfo
+                    //   function takes a boolean as an argument ("addMateCigar") and will add/update the mate cigar if
+                    //   set to true.  This is the one you want to use.
+                    SamPairUtil.setMateInfo(mate.record, newRead, null, true);
                     if ( reQueueMate ) waitingReads.add(mate.record);
                 }
 
diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
index 46c6efb0c..c5bfd4731 100644
--- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
+++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
@@ -61,8 +61,8 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
     private static final String knownIndels = validationDataLocation + "indelRealignerTest.pilot1.ceu.vcf";
     private static final String baseCommandPrefix = "-T IndelRealigner -noPG -R " + b36KGReference + " -I " + mainTestBam + " -targetIntervals " + mainTestIntervals + " -compress 0 -L 20:49,500-55,500 ";
     private static final String baseCommand = baseCommandPrefix + "-o %s ";
-    private static final String base_md5 = "a102dd55451799e5f053c784b762087e";
-    private static final String base_md5_with_SW_or_VCF = "06b8eefcbd785e929027feaa22bb060d";
+    private static final String base_md5 = "458588d68c8ea7e54443ea722604b265";
+    private static final String base_md5_with_SW_or_VCF = "d5ed91bd5b2023c69078a0fc00268d3c";
 
     @Test
     public void testDefaults() {
@@ -85,7 +85,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
         WalkerTestSpec spec1 = new WalkerTestSpec(
                 baseCommand + "--consensusDeterminationModel KNOWNS_ONLY -known " + knownIndels,
                 1,
-                Arrays.asList("1b24b0f2a20aed1adc726d1b296a3192"));
+                Arrays.asList("a1b9396f4d5b65f7ae6e0062daf363a3"));
         executeTest("realigner known indels only from VCF", spec1);
     }
 
@@ -102,7 +102,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
     public void testLods() {
         HashMap<String, String> e = new HashMap<String, String>();
         e.put("-LOD 60", base_md5);
-        e.put( "-LOD 1 --consensusDeterminationModel USE_SW",  "4bf28d3c0337682d439257874377a681" );
+        e.put( "-LOD 1 --consensusDeterminationModel USE_SW",  "dea9bd14323b33348d9cf28e256415f2" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@@ -118,7 +118,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T IndelRealigner -noPG -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10,000,000-11,000,000 -targetIntervals " + validationDataLocation + "indelRealignerTest.NA12878.chrom1.intervals -compress 0 -o %s",
                 1,
-                Arrays.asList("f4f6c3b2a2be0306a0ecd3def334bafe"));
+                Arrays.asList("b91c0bf803247f703dc1cb6ccdc4f18f"));
         executeTest("realigner long run", spec);
     }
 
@@ -127,7 +127,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseCommand + "--noOriginalAlignmentTags --consensusDeterminationModel USE_SW",
                 1,
-                Arrays.asList("71fb521f8febfe2dc683fc636e28ae7d"));
+                Arrays.asList("041e2254f271261fb46dc3878cf638f6"));
         executeTest("realigner no output tags", spec);
     }
 
@@ -149,7 +149,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
     @Test
     public void testMaxReadsInMemory() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put("--maxReadsInMemory 10000", base_md5);
+        e.put("--maxReadsInMemory 10000", "0108cd5950f1a4eb90209c3dca8f9e11");
         e.put( "--maxReadsInMemory 40000", base_md5 );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {