diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java
index 3277f5060..6a3d755d7 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java
@@ -125,4 +125,14 @@ public class ValidateVariantsIntegrationTest extends WalkerTest {
         executeTest("test bad ref allele in deletion", spec);
     }
 
+    @Test
+    public void testComplexEvents() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                baseTestString("complexEvents.vcf", "ALL"),
+                0,
+                Arrays.asList("d41d8cd98f00b204e9800998ecf8427e")
+        );
+
+        executeTest("test validating complex events", spec);
+    }
 }
diff --git a/public/java/test/org/broadinstitute/sting/utils/HaplotypeUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/HaplotypeUnitTest.java
index ec08d97c5..161eefa8f 100644
--- a/public/java/test/org/broadinstitute/sting/utils/HaplotypeUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/HaplotypeUnitTest.java
@@ -53,11 +53,11 @@ public class HaplotypeUnitTest extends BaseTest {
         h1CigarList.add(new CigarElement(bases.length(), CigarOperator.M));
         final Cigar h1Cigar = new Cigar(h1CigarList);
         String h1bases = "AACTTCTGGTCAACTGGTCAACTGGTCAACTGGTCA";
-        basicInsertTest("-", "ACTT", 1, h1Cigar, bases, h1bases);
+        basicInsertTest("A", "AACTT", 1, h1Cigar, bases, h1bases);
         h1bases = "ACTGGTCACTTAACTGGTCAACTGGTCAACTGGTCA";
-        basicInsertTest("-", "ACTT", 7, h1Cigar, bases, h1bases);
+        basicInsertTest("A", "AACTT", 7, h1Cigar, bases, h1bases);
         h1bases = "ACTGGTCAACTGGTCAAACTTCTGGTCAACTGGTCA";
-        basicInsertTest("-", "ACTT", 17, h1Cigar, bases, h1bases);
+        basicInsertTest("A", "AACTT", 17, h1Cigar, bases, h1bases);
     }
 
     @Test
@@ -68,11 +68,11 @@ public class HaplotypeUnitTest extends BaseTest {
         h1CigarList.add(new CigarElement(bases.length(), CigarOperator.M));
         final Cigar h1Cigar = new Cigar(h1CigarList);
         String h1bases = "ATCAACTGGTCAACTGGTCAACTGGTCA";
-        basicInsertTest("ACTT", "-", 1, h1Cigar, bases, h1bases);
+        basicInsertTest("AACTT", "A", 1, h1Cigar, bases, h1bases);
         h1bases = "ACTGGTCGGTCAACTGGTCAACTGGTCA";
-        basicInsertTest("ACTT", "-", 7, h1Cigar, bases, h1bases);
+        basicInsertTest("AACTT", "A", 7, h1Cigar, bases, h1bases);
         h1bases = "ACTGGTCAACTGGTCAATCAACTGGTCA";
-        basicInsertTest("ACTT", "-", 17, h1Cigar, bases, h1bases);
+        basicInsertTest("AACTT", "A", 17, h1Cigar, bases, h1bases);
     }
 
     @Test
@@ -102,11 +102,11 @@ public class HaplotypeUnitTest extends BaseTest {
         h1CigarList.add(new CigarElement(7 + 4, CigarOperator.M));
         final Cigar h1Cigar = new Cigar(h1CigarList);
         String h1bases = "AACTTTCG" + "CCGGCCGGCC" + "ATCGATCG" + "AGGGGGA" + "AGGC";
-        basicInsertTest("-", "ACTT", 1, h1Cigar, bases, h1bases);
+        basicInsertTest("A", "AACTT", 1, h1Cigar, bases, h1bases);
         h1bases = "ATCG" + "CCGGCCGGCC" + "ATCACTTGATCG" + "AGGGGGA" + "AGGC";
-        basicInsertTest("-", "ACTT", 7, h1Cigar, bases, h1bases);
+        basicInsertTest("A", "AACTT", 7, h1Cigar, bases, h1bases);
         h1bases = "ATCG" + "CCGGCCGGCC" + "ATCGATCG" + "AGACTTGGGGA" + "AGGC";
-        basicInsertTest("-", "ACTT", 17, h1Cigar, bases, h1bases);
+        basicInsertTest("A", "AACTT", 17, h1Cigar, bases, h1bases);
     }
 
     @Test
@@ -121,11 +121,11 @@ public class HaplotypeUnitTest extends BaseTest {
         h1CigarList.add(new CigarElement(7 + 4, CigarOperator.M));
         final Cigar h1Cigar = new Cigar(h1CigarList);
         String h1bases = "A" + "CGGCCGGCC" + "ATCGATCG" + "AGGGGGA" + "AGGC";
-        basicInsertTest("ACTT", "-", 1, h1Cigar, bases, h1bases);
+        basicInsertTest("AACTT", "A", 1, h1Cigar, bases, h1bases);
         h1bases = "ATCG" + "CCGGCCGGCC" + "ATCG" + "AGGGGGA" + "AGGC";
-        basicInsertTest("ACTT", "-", 7, h1Cigar, bases, h1bases);
+        basicInsertTest("AACTT", "A", 7, h1Cigar, bases, h1bases);
         h1bases = "ATCG" + "CCGGCCGGCC" + "ATCGATCG" + "AGA" + "AGGC";
-        basicInsertTest("ACTT", "-", 17, h1Cigar, bases, h1bases);
+        basicInsertTest("AACTT", "A", 17, h1Cigar, bases, h1bases);
     }
 
     @Test
diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContextUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContextUnitTest.java
index 6f5756bdc..8f03f1d38 100644
--- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContextUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContextUnitTest.java
@@ -56,7 +56,7 @@ public class VariantJEXLContextUnitTest extends BaseTest {
 
     Allele A, Aref, T, Tref;
 
-    Allele del, delRef, ATC, ATCref;
+    Allele ATC, ATCref;
     // A [ref] / T at 10
 
     GenomeLoc snpLoc;
@@ -84,9 +84,6 @@ public class VariantJEXLContextUnitTest extends BaseTest {
 
     @BeforeMethod
     public void before() {
-        del = Allele.create("-");
-        delRef = Allele.create("-", true);
-
         A = Allele.create("A");
         Aref = Allele.create("A", true);
         T = Allele.create("T");