diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java
index faff99f3e..5ad213903 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java
@@ -315,7 +315,7 @@ public class DepthOfCoverageStats {
 
     public int value2bin(int value) {
         for ( int index = 0; index < binLeftEndpoints.length; index++ ) {
-            if ( binLeftEndpoints[index] >= value ) {
+            if ( binLeftEndpoints[index] > value ) {
                 return index;
             }
         }
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageB36IntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageB36IntegrationTest.java
index e86a241d5..043b2eaf2 100644
--- a/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageB36IntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageB36IntegrationTest.java
@@ -65,9 +65,9 @@ public class DepthOfCoverageB36IntegrationTest extends WalkerTest {
         spec.addAuxFile("6b15f5330414b6d4e2f6caea42139fa1", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_counts"));
         spec.addAuxFile("cc6640d82077991dde8a2b523935cdff", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_proportions"));
         spec.addAuxFile("0fb627234599c258a3fee1b2703e164a", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_statistics"));
-        spec.addAuxFile("3ad34680c216279c52c7fa0c9e078249", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary"));
+        spec.addAuxFile("cb73a0fa0cee50f1fb8f249315d38128", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary"));
         spec.addAuxFile("347b47ef73fbd4e277704ddbd7834f69", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_statistics"));
-        spec.addAuxFile("65bc90b4839cb9f20e60aba4956f06a9", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_summary"));
+        spec.addAuxFile("4ec920335d4b9573f695c39d62748089", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_summary"));
 
         execute("testMapQ0Only",spec);
     }
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java
index 216753be9..59ac1a41e 100644
--- a/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java
@@ -59,21 +59,21 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest {
         spec.addAuxFile("9df5e7e07efeb34926c94a724714c219", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_counts"));
         spec.addAuxFile("b9a7748e5aec4dc06daed893c901c00d", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_proportions"));
         spec.addAuxFile("9cd395f47b329b9dd00ad024fcac9929", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_statistics"));
-        spec.addAuxFile("ca95d2508366d32bf91bf0b0009a023a", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_summary"));
+        spec.addAuxFile("aec669d64d9dd652dd088a5341835ea5", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_summary"));
         spec.addAuxFile("f6dbd74d32a48abe71ce08d300bce983", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_statistics"));
-        spec.addAuxFile("7962a7c09c43ff8b339fa52bce51bfca", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_summary"));
+        spec.addAuxFile("e3a3467ed259ee3680f8d01980f525b7", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_summary"));
         spec.addAuxFile("b82846df660f0aac8429aec57c2a62d6", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_cumulative_coverage_counts"));
         spec.addAuxFile("d32a8c425fadcc4c048bd8b48d0f61e5", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_cumulative_coverage_proportions"));
         spec.addAuxFile("7b9d0e93bf5b5313995be7010ef1f528", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_statistics"));
-        spec.addAuxFile("755463d88222c81b84f99615e7b4cfd6", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_summary"));
+        spec.addAuxFile("2aae346204c5f15517158da8e61a6c16", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_summary"));
         spec.addAuxFile("e70952f241eebb9b5448f2e7cb288131", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_statistics"));
-        spec.addAuxFile("51e4c04dfcb4a20c552ca6f013977fa8", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_summary"));
+        spec.addAuxFile("054ed1e184f46d6a170dc9bf6524270c", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_summary"));
         spec.addAuxFile("d53431022f7387fe9ac47814ab1fcd88", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_counts"));
         spec.addAuxFile("650ee3714da7fbad7832c9d4ad49eb51", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_proportions"));
         spec.addAuxFile("df0ba76e0e6082c0d29fcfd68efc6b77", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_statistics"));
-        spec.addAuxFile("a52395c883ce8f1a62444d214fe37e88", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary"));
+        spec.addAuxFile("7dcac2e8962c778081486332a4576dc3", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary"));
         spec.addAuxFile("a50011571334f17e950ad3ed1149e350", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_statistics"));
-        spec.addAuxFile("f12a5f97b69718333c4987e3beb98f06", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_summary"));
+        spec.addAuxFile("6f3260504295695d765af639539585c9", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_summary"));
         
         execute("testBaseOutputNoFiltering",spec);
     }
diff --git a/scala/qscript/playground/BatchMerge.q b/scala/qscript/playground/BatchMerge.q
index 2804e2df0..e0102cd70 100755
--- a/scala/qscript/playground/BatchMerge.q
+++ b/scala/qscript/playground/BatchMerge.q
@@ -24,6 +24,7 @@ class batchMergePipeline extends QScript {
   @Hidden @Argument(doc="Min map q",shortName="mmq",required=false) var mmq : Int = 20
   @Hidden @Argument(doc="Max mismatching bases",shortName="mmb",required=false) var mmb : Int = 3
   @Hidden @Argument(doc="baq gap open penalty, using sets baq to calc when necessary",shortName="baqp",required=false) var baq : Int = -1
+  @Hidden @Argument(doc="VCFs are indels",shortName="indel") var indelMode : Boolean = false
 
   def script = {
 
@@ -61,6 +62,9 @@ class batchMergePipeline extends QScript {
       this.scatterCount = 60
       this.output_mode = Some(UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_ALL_SITES)
       this.genotyping_mode = Some(GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES)
+      if ( batchMerge.indelMode ) {
+        this.genotype_likelihoods_model = Some(GenotypeLikelihoodsCalculationModel.Model.DINDEL)
+      }
     }
 
     def newUGCL( bams: (List[File],Int) ) : UGCalcLikelihoods = {
@@ -81,6 +85,9 @@ class batchMergePipeline extends QScript {
       this.memoryLimit = Some(8)
       this.output_mode = Some(UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_ALL_SITES)
       this.genotyping_mode = Some(GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES)
+      if ( batchMerge.indelMode ) {
+        this.genotype_likelihoods_model = Some(GenotypeLikelihoodsCalculationModel.Model.DINDEL)
+      }
     }
 
     var cVars : UGCallVariants = new UGCallVariants with CallVariantsArgs