diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Path.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Path.java
index f232a4ce0..47676a498 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Path.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Path.java
@@ -86,7 +86,7 @@ public class Path<T extends BaseVertex> {
 
     // used in the bubble state machine to apply Smith-Waterman to the bubble sequence
     // these values were chosen via optimization against the NA12878 knowledge base
-    public static final Parameters NEW_SW_PARAMETERS = new Parameters(10, -20.0, -26.0, -0.1);
+    public static final Parameters NEW_SW_PARAMETERS = new Parameters(20.0, -15.0, -26.0, -1.1);
 
     private static final byte[] STARTING_SW_ANCHOR_BYTES = "XXXXXXXXX".getBytes();
 
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
index 500db6ae9..2664f3ed0 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
@@ -166,7 +166,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     @Test
     public void HCTestStructuralIndels() {
         final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, privateTestDir + "AFR.structural.indels.bam") + " --no_cmdline_in_header -o %s -minPruning 6 -L 20:8187565-8187800 -L 20:18670537-18670730";
-        final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("cac0d88fa4471c7a0ac96533a9a6354b"));
+        final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("eb5772b825120a0b8710e5add485d73a"));
         executeTest("HCTestStructuralIndels: ", spec);
     }
 
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KBestPathsUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KBestPathsUnitTest.java
index 302866b55..d1bae74b2 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KBestPathsUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KBestPathsUnitTest.java
@@ -425,7 +425,7 @@ public class KBestPathsUnitTest extends BaseTest {
         logger.warn("AltPath : " + altPath + " cigar " + altPath.calculateCigar());
 
         Assert.assertEquals(refPath.calculateCigar().toString(), "51M");
-        Assert.assertEquals(altPath.calculateCigar().toString(), "3M14D2M20I32M");
+        Assert.assertEquals(altPath.calculateCigar().toString(), "3M6I48M");
     }
 
     // -----------------------------------------------------------------
@@ -443,7 +443,7 @@ public class KBestPathsUnitTest extends BaseTest {
                 Arrays.asList("G", "C", "1M"),
                 Arrays.asList("G", "", "1D"),
                 Arrays.asList("", "C", "1I"),
-                Arrays.asList("AAA", "CGT", "3D3I"),
+                Arrays.asList("AAA", "CGT", "3M"),
                 Arrays.asList("TAT", "CAC", "3M"),
                 Arrays.asList("GCTG", "GTCG", "4M"),
                 Arrays.asList("AAAAA", "", "5D"),