diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java
index d820ea259..9544aaac4 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java
@@ -94,7 +94,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
     @Test
     public void testHaplotypeCallerMultiSampleGGAMultiAllelic() {
         HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:133041-133161 -L 20:300207-300337",
-                "3c02e454fe6d0e296effd99fbd3cba4c");
+                "1a65d432437670d2816a42ea270c06a1");
     }
 
     private void HCTestComplexConsensusMode(String bam, String args, String md5) {
@@ -106,7 +106,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
     @Test
     public void testHaplotypeCallerMultiSampleConsensusModeComplex() {
         HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:119673-119823 -L 20:121408-121538 -L 20:133041-133161 -L 20:300207-300337",
-                "f0560ba2ca20e5202181d0e57b1ee8cf");
+                "a5bb8f7eb1f7db997be9fd8928a788f6");
     }
 
 }
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
index 77fbed95b..89b68114f 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
@@ -67,9 +67,9 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
         final String WExIntervals = "-L 20:10,000,000-10,100,000 -isr INTERSECTION -L " + hg19Chr20Intervals;
 
         // this functionality can be adapted to provide input data for whatever you might want in your data
-        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "f321fadf3d6b4608536fba1015e9693a"});
-        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "8d5626262b255ce6d4a53394ea8cd30f"});
-        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "126c94d06e00c67380051c4924054841"});
+        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "9db87ae56df22456f3c08024384f3e5e"});
+        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "4a006f9e39cacc3ae84384ad56ca22a2"});
+        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "cb048cbfa5cc058d680f9be5fd689767"});
         tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "d5c07fa3edca496a84fd17cecad06230"});
         tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "330685c734e277d70a44637de85ad54d"});
         tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "e6ec90da053a612f0c615e221eb34baa"});
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
index 9993764a9..72c47b8ba 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
@@ -227,7 +227,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     public void HCTestDBSNPAnnotationWGS() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,000,000-10,100,000 -D " + b37dbSNP132, 1,
-                Arrays.asList("10a7a3d49cb6cb172ae8404996c524df"));
+                Arrays.asList("3d1fcf8b4a1d8d328c0a0aae5f4558eb"));
         executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec);
     }
 
@@ -244,7 +244,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     public void HCTestDBSNPAnnotationWGSGraphBased() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T HaplotypeCaller -likelihoodEngine GraphBased --disableDithering --pcr_indel_model NONE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,000,000-10,100,000 -D " + b37dbSNP132, 1,
-                Arrays.asList("14384fe06359bf35e11d3802217e1a23"));
+                Arrays.asList("fc2e81d02c6bbf15147a46797402fda7"));
         executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec);
     }
 
@@ -276,7 +276,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     public void HCTestAggressivePcrIndelModelWGS() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T HaplotypeCaller --disableDithering --pcr_indel_model AGGRESSIVE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_BAM + " -o %s -L 20:10,000,000-10,300,000", 1,
-                Arrays.asList("daf2a533d83f1a5fd7d0e5a92d67fd64"));
+                Arrays.asList("a97154c320a04f3e21f23b8c793d4111"));
         executeTest("HC calling with aggressive indel error modeling on WGS intervals", spec);
     }
 
@@ -284,7 +284,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     public void HCTestConservativePcrIndelModelWGS() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T HaplotypeCaller --disableDithering --pcr_indel_model CONSERVATIVE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_BAM + " -o %s -L 20:10,000,000-10,300,000", 1,
-                Arrays.asList("69bccf72c900361775d076d7d131955d"));
+                Arrays.asList("df871f2b5cbb01bdc758614ef1923bf7"));
         executeTest("HC calling with conservative indel error modeling on WGS intervals", spec);
     }
 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java
index 320ba1e09..8a91e649e 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java
@@ -60,7 +60,7 @@ public class HaplotypeCallerParallelIntegrationTest extends WalkerTest {
         List<Object[]> tests = new ArrayList<>();
 
         for ( final int nct : Arrays.asList(1, 2, 4) ) {
-            tests.add(new Object[]{nct, "af29c396835b86d88f366629884e6ba4"});
+            tests.add(new Object[]{nct, "faaf2217a920225b6937d87e949d1a68"});
         }
 
         return tests.toArray(new Object[][]{});
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/haplotype/EventMap.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/haplotype/EventMap.java
index 8cd2a692e..a540054bc 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/haplotype/EventMap.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/haplotype/EventMap.java
@@ -193,14 +193,17 @@ public class EventMap extends TreeMap<Integer, VariantContext> {
      * @return true if the cigar is too complex, false otherwise
      */
     private boolean variationIsTooComplex(final List<VariantContext> events) {
-        int indelCount = 0;
-        for ( final VariantContext event : events ) {
-            if ( event.isIndel() )
-                indelCount++;
-        }
+        // TODO -- we've decided to disable this for now and try "physical phasing"
+        return false;
 
+        //int indelCount = 0;
+        //for ( final VariantContext event : events ) {
+        //    if ( event.isIndel() )
+        //        indelCount++;
+        //}
+        //
         // don't allow too many indels
-        return indelCount > MAX_INDELS_PER_HAPLOTYPE;
+        //return indelCount > MAX_INDELS_PER_HAPLOTYPE;
     }
 
     /**