diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
index 8738def50..d91df82e2 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
@@ -217,7 +217,7 @@ public class GenotypingEngine {
         }
 
         cleanUpSymbolicUnassembledEvents( haplotypes );
-        if( activeAllelesToGenotype.isEmpty() && haplotypes.get(0).getSampleKeySet().size() >= 3 ) { // if not in GGA mode and have at least 3 samples try to create MNP and complex events by looking at LD structure
+        if( activeAllelesToGenotype.isEmpty() && haplotypes.get(0).getSampleKeySet().size() >= 10 ) { // if not in GGA mode and have at least 10 samples try to create MNP and complex events by looking at LD structure
             mergeConsecutiveEventsBasedOnLD( haplotypes, startPosKeySet, ref, refLoc );
         }
         if( !activeAllelesToGenotype.isEmpty() ) { // we are in GGA mode!
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
index 62554c4ab..e90d89a8c 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
@@ -139,7 +139,7 @@ public class LikelihoodCalculationEngine {
     }
 
     private static int computeFirstDifferingPosition( final byte[] b1, final byte[] b2 ) {
-        for( int iii = 0; iii < b1.length && iii < b2.length; iii++ ){
+        for( int iii = 0; iii < b1.length && iii < b2.length; iii++ ) {
             if( b1[iii] != b2[iii] ) {
                 return iii;
             }
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 1d4fad19e..a0849d0c1 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
@@ -42,7 +42,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
 
     @Test
     public void testHaplotypeCallerMultiSampleComplex() {
-        HCTestComplexVariants(CEUTRIO_BAM, "", "30598abeeb0b0ae5816ffdbf0c4044fd");
+        HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "966d338f423c86a390d685aa6336ec69");
     }
 
     private void HCTestSymbolicVariants(String bam, String args, String md5) {
@@ -94,6 +94,4 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
                 Arrays.asList("79af83432dc4a1768b3ebffffc4d2b8f"));
         executeTest("HC calling on a ReducedRead BAM", spec);
     }
-
-
 }