diff --git a/CHANGELOG.md b/CHANGELOG.md
index a54814f2cb7affcf8472c6f50ae213bb5eef1202..e975fc257b08f53ab1e5081b01d3f397126d999d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,9 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## Unreleased
+### Added
+- Option in merge_vcf_files.py to merge VCF files of different samples without genotyping based on read depth computed by duphold
+- Option in vcf_to_table.py to calculate number of deletions that are supported by a change in read depth compared to 1000 bp flanking regions
 
 ## [0.3.0] - 2019-12-16
 ### Added
diff --git a/scripts/.idea/workspace.xml b/scripts/.idea/workspace.xml
index 129471360ed376b28b3bbfdbdc2f4cec2c6defdd..39ed2b8058a20e2de6d60ae898e781e7b7085cac 100644
--- a/scripts/.idea/workspace.xml
+++ b/scripts/.idea/workspace.xml
@@ -3,6 +3,8 @@
   <component name="ChangeListManager">
     <list default="true" id="38800356-6f91-47c6-8c6a-4d9b650fe843" name="Default" comment="">
       <change beforePath="$PROJECT_DIR$/.idea/workspace.xml" afterPath="$PROJECT_DIR$/.idea/workspace.xml" />
+      <change beforePath="$PROJECT_DIR$/convert/vcf_to_table.py" afterPath="$PROJECT_DIR$/convert/vcf_to_table.py" />
+      <change beforePath="$PROJECT_DIR$/genotype/merge_vcf_files.py" afterPath="$PROJECT_DIR$/genotype/merge_vcf_files.py" />
     </list>
     <option name="EXCLUDED_CONVERTED_TO_IGNORED" value="true" />
     <option name="TRACKING_ENABLED" value="true" />
@@ -11,62 +13,26 @@
     <option name="HIGHLIGHT_NON_ACTIVE_CHANGELIST" value="false" />
     <option name="LAST_RESOLUTION" value="IGNORE" />
   </component>
+  <component name="DatabaseView">
+    <option name="SHOW_INTERMEDIATE" value="true" />
+    <option name="GROUP_DATA_SOURCES" value="true" />
+    <option name="GROUP_SCHEMA" value="true" />
+    <option name="GROUP_CONTENTS" value="false" />
+    <option name="SORT_POSITIONED" value="false" />
+    <option name="SHOW_TABLE_DETAILS" value="true" />
+    <option name="SHOW_EMPTY_GROUPS" value="false" />
+    <option name="AUTO_SCROLL_FROM_SOURCE" value="false" />
+    <expand />
+    <select />
+  </component>
   <component name="FileEditorManager">
     <leaf SIDE_TABS_SIZE_LIMIT_KEY="300">
-      <file leaf-file-name="merge_vcf_files.py" pinned="false" current-in-tab="false">
-        <entry file="file://$PROJECT_DIR$/genotype/merge_vcf_files.py">
-          <provider selected="true" editor-type-id="text-editor">
-            <state relative-caret-position="7272">
-              <caret line="414" column="31" lean-forward="false" selection-start-line="414" selection-start-column="4" selection-end-line="414" selection-end-column="31" />
-              <folding>
-                <element signature="e#132#147#0" expanded="true" />
-              </folding>
-            </state>
-          </provider>
-        </entry>
-      </file>
-      <file leaf-file-name="predict_cnvs_model_insertions_probabilities.py" pinned="false" current-in-tab="false">
-        <entry file="file://$PROJECT_DIR$/predict/predict_cnvs_model_insertions_probabilities.py">
-          <provider selected="true" editor-type-id="text-editor">
-            <state relative-caret-position="1026">
-              <caret line="60" column="8" lean-forward="false" selection-start-line="60" selection-start-column="8" selection-end-line="60" selection-end-column="8" />
-              <folding>
-                <element signature="e#112#131#0" expanded="true" />
-              </folding>
-            </state>
-          </provider>
-        </entry>
-      </file>
-      <file leaf-file-name="process_simple_cnvs.py" pinned="false" current-in-tab="false">
-        <entry file="file://$PROJECT_DIR$/process/process_simple_cnvs.py">
-          <provider selected="true" editor-type-id="text-editor">
-            <state relative-caret-position="936">
-              <caret line="59" column="4" lean-forward="false" selection-start-line="59" selection-start-column="4" selection-end-line="59" selection-end-column="4" />
-              <folding>
-                <element signature="e#120#135#0" expanded="true" />
-              </folding>
-            </state>
-          </provider>
-        </entry>
-      </file>
-      <file leaf-file-name="internally_collapse_bedpe_intervals.py" pinned="false" current-in-tab="false">
-        <entry file="file://$PROJECT_DIR$/collapse/internally_collapse_bedpe_intervals.py">
-          <provider selected="true" editor-type-id="text-editor">
-            <state relative-caret-position="3636">
-              <caret line="210" column="40" lean-forward="false" selection-start-line="210" selection-start-column="40" selection-end-line="210" selection-end-column="40" />
-              <folding />
-            </state>
-          </provider>
-        </entry>
-      </file>
-      <file leaf-file-name="filter_ref_sites_vcf.py" pinned="false" current-in-tab="true">
+      <file leaf-file-name="filter_ref_sites_vcf.py" pinned="false" current-in-tab="false">
         <entry file="file://$PROJECT_DIR$/filter/filter_ref_sites_vcf.py">
           <provider selected="true" editor-type-id="text-editor">
-            <state relative-caret-position="18">
+            <state relative-caret-position="198">
               <caret line="11" column="0" lean-forward="false" selection-start-line="11" selection-start-column="0" selection-end-line="11" selection-end-column="0" />
-              <folding>
-                <element signature="e#154#169#0" expanded="true" />
-              </folding>
+              <folding />
             </state>
           </provider>
         </entry>
@@ -93,11 +59,23 @@
           </provider>
         </entry>
       </file>
+      <file leaf-file-name="merge_vcf_files.py" pinned="false" current-in-tab="true">
+        <entry file="file://$PROJECT_DIR$/genotype/merge_vcf_files.py">
+          <provider selected="true" editor-type-id="text-editor">
+            <state relative-caret-position="521">
+              <caret line="102" column="34" lean-forward="true" selection-start-line="102" selection-start-column="34" selection-end-line="102" selection-end-column="34" />
+              <folding>
+                <element signature="e#132#147#0" expanded="true" />
+              </folding>
+            </state>
+          </provider>
+        </entry>
+      </file>
       <file leaf-file-name="vcf_to_table.py" pinned="false" current-in-tab="false">
         <entry file="file://$PROJECT_DIR$/convert/vcf_to_table.py">
           <provider selected="true" editor-type-id="text-editor">
-            <state relative-caret-position="2376">
-              <caret line="135" column="0" lean-forward="false" selection-start-line="135" selection-start-column="0" selection-end-line="145" selection-end-column="0" />
+            <state relative-caret-position="1602">
+              <caret line="152" column="78" lean-forward="false" selection-start-line="152" selection-start-column="78" selection-end-line="152" selection-end-column="78" />
               <folding>
                 <element signature="e#108#123#0" expanded="true" />
               </folding>
@@ -144,6 +122,7 @@
       <find>structural_variant_from</find>
       <find>keys</find>
       <find>.keys</find>
+      <find>genotyping</find>
     </findStrings>
   </component>
   <component name="Git.Settings">
@@ -178,12 +157,12 @@
         <option value="$PROJECT_DIR$/convert/intersect_bedpe_to_feature_bedpe.py" />
         <option value="$PROJECT_DIR$/filter/concat_duphold_to_calls.py" />
         <option value="$PROJECT_DIR$/convert/bedpe_to_vcf.py" />
-        <option value="$PROJECT_DIR$/convert/vcf_to_table.py" />
-        <option value="$PROJECT_DIR$/genotype/merge_vcf_files.py" />
         <option value="$PROJECT_DIR$/collapse/internally_collapse_bedpe_intervals.py" />
         <option value="$PROJECT_DIR$/intersect/intersecting_bedpe_intervals.py" />
         <option value="$PROJECT_DIR$/filter/filter_ref_sites_vcf.py" />
         <option value="$PROJECT_DIR$/convert/vcf_to_site_only_vcf.py" />
+        <option value="$PROJECT_DIR$/convert/vcf_to_table.py" />
+        <option value="$PROJECT_DIR$/genotype/merge_vcf_files.py" />
       </list>
     </option>
   </component>
@@ -215,7 +194,6 @@
       <foldersAlwaysOnTop value="true" />
     </navigator>
     <panes>
-      <pane id="Scratches" />
       <pane id="Scope" />
       <pane id="ProjectPane">
         <subPane>
@@ -278,12 +256,13 @@
           <select />
         </subPane>
       </pane>
+      <pane id="Scratches" />
     </panes>
   </component>
   <component name="PropertiesComponent">
     <property name="nodejs_interpreter_path.stuck_in_default_project" value="undefined stuck path" />
     <property name="WebServerToolWindowFactoryState" value="false" />
-    <property name="last_opened_file_path" value="$USER_HOME$/Code/PycharmProjects/Polyhetero" />
+    <property name="last_opened_file_path" value="$PROJECT_DIR$" />
   </component>
   <component name="RunDashboard">
     <option name="ruleStates">
@@ -323,10 +302,10 @@
       <window_info id="Python Console" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.32914045" sideWeight="0.5" order="7" side_tool="false" content_ui="tabs" />
       <window_info id="Run" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="2" side_tool="false" content_ui="tabs" />
       <window_info id="Terminal" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.32914045" sideWeight="0.5" order="7" side_tool="false" content_ui="tabs" />
-      <window_info id="Project" active="false" anchor="left" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="true" show_stripe_button="true" weight="0.42999446" sideWeight="0.5" order="0" side_tool="false" content_ui="combo" />
+      <window_info id="Project" active="false" anchor="left" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="true" show_stripe_button="true" weight="0.44659656" sideWeight="0.5" order="0" side_tool="false" content_ui="combo" />
       <window_info id="Docker" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="false" weight="0.33" sideWeight="0.5" order="7" side_tool="false" content_ui="tabs" />
-      <window_info id="Database" active="false" anchor="right" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="3" side_tool="false" content_ui="tabs" />
-      <window_info id="SciView" active="false" anchor="right" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="3" side_tool="false" content_ui="tabs" />
+      <window_info id="Database" active="false" anchor="right" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.32982844" sideWeight="0.5125786" order="4" side_tool="true" content_ui="tabs" />
+      <window_info id="SciView" active="false" anchor="right" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.32982844" sideWeight="0.4874214" order="3" side_tool="false" content_ui="tabs" />
       <window_info id="Structure" active="false" anchor="left" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.25" sideWeight="0.5" order="1" side_tool="false" content_ui="tabs" />
       <window_info id="Favorites" active="false" anchor="left" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="2" side_tool="true" content_ui="tabs" />
       <window_info id="Debug" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.4" sideWeight="0.5" order="3" side_tool="false" content_ui="tabs" />
@@ -598,40 +577,31 @@
         </state>
       </provider>
     </entry>
-    <entry file="file://$PROJECT_DIR$/genotype/merge_vcf_files.py">
+    <entry file="file://$PROJECT_DIR$/collapse/internally_collapse_bedpe_intervals.py">
       <provider selected="true" editor-type-id="text-editor">
-        <state relative-caret-position="7272">
-          <caret line="414" column="31" lean-forward="false" selection-start-line="414" selection-start-column="4" selection-end-line="414" selection-end-column="31" />
-          <folding>
-            <element signature="e#132#147#0" expanded="true" />
-          </folding>
+        <state relative-caret-position="866">
+          <caret line="210" column="40" lean-forward="false" selection-start-line="210" selection-start-column="40" selection-end-line="210" selection-end-column="40" />
         </state>
       </provider>
     </entry>
-    <entry file="file://$PROJECT_DIR$/predict/predict_cnvs_model_insertions_probabilities.py">
+    <entry file="file://$PROJECT_DIR$/process/process_simple_cnvs.py">
       <provider selected="true" editor-type-id="text-editor">
-        <state relative-caret-position="1026">
-          <caret line="60" column="8" lean-forward="false" selection-start-line="60" selection-start-column="8" selection-end-line="60" selection-end-column="8" />
-          <folding>
-            <element signature="e#112#131#0" expanded="true" />
-          </folding>
+        <state relative-caret-position="866">
+          <caret line="59" column="4" lean-forward="false" selection-start-line="59" selection-start-column="4" selection-end-line="59" selection-end-column="4" />
         </state>
       </provider>
     </entry>
-    <entry file="file://$PROJECT_DIR$/process/process_simple_cnvs.py">
+    <entry file="file://$PROJECT_DIR$/predict/predict_cnvs_model_insertions_probabilities.py">
       <provider selected="true" editor-type-id="text-editor">
-        <state relative-caret-position="936">
-          <caret line="59" column="4" lean-forward="false" selection-start-line="59" selection-start-column="4" selection-end-line="59" selection-end-column="4" />
-          <folding>
-            <element signature="e#120#135#0" expanded="true" />
-          </folding>
+        <state relative-caret-position="866">
+          <caret line="60" column="8" lean-forward="false" selection-start-line="60" selection-start-column="8" selection-end-line="60" selection-end-column="8" />
         </state>
       </provider>
     </entry>
-    <entry file="file://$PROJECT_DIR$/collapse/internally_collapse_bedpe_intervals.py">
+    <entry file="file://$PROJECT_DIR$/filter/filter_ref_sites_vcf.py">
       <provider selected="true" editor-type-id="text-editor">
-        <state relative-caret-position="3636">
-          <caret line="210" column="40" lean-forward="false" selection-start-line="210" selection-start-column="40" selection-end-line="210" selection-end-column="40" />
+        <state relative-caret-position="198">
+          <caret line="11" column="0" lean-forward="false" selection-start-line="11" selection-start-column="0" selection-end-line="11" selection-end-column="0" />
           <folding />
         </state>
       </provider>
@@ -646,6 +616,16 @@
         </state>
       </provider>
     </entry>
+    <entry file="file://$PROJECT_DIR$/gridss/fix_gridss_header.py">
+      <provider selected="true" editor-type-id="text-editor">
+        <state relative-caret-position="648">
+          <caret line="38" column="34" lean-forward="false" selection-start-line="38" selection-start-column="34" selection-end-line="38" selection-end-column="34" />
+          <folding>
+            <element signature="e#68#83#0" expanded="true" />
+          </folding>
+        </state>
+      </provider>
+    </entry>
     <entry file="file://$PROJECT_DIR$/convert/vcf_to_bedpe.py">
       <provider selected="true" editor-type-id="text-editor">
         <state relative-caret-position="108">
@@ -656,30 +636,20 @@
     </entry>
     <entry file="file://$PROJECT_DIR$/convert/vcf_to_table.py">
       <provider selected="true" editor-type-id="text-editor">
-        <state relative-caret-position="2376">
-          <caret line="135" column="0" lean-forward="false" selection-start-line="135" selection-start-column="0" selection-end-line="145" selection-end-column="0" />
+        <state relative-caret-position="1602">
+          <caret line="152" column="78" lean-forward="false" selection-start-line="152" selection-start-column="78" selection-end-line="152" selection-end-column="78" />
           <folding>
             <element signature="e#108#123#0" expanded="true" />
           </folding>
         </state>
       </provider>
     </entry>
-    <entry file="file://$PROJECT_DIR$/gridss/fix_gridss_header.py">
-      <provider selected="true" editor-type-id="text-editor">
-        <state relative-caret-position="648">
-          <caret line="38" column="34" lean-forward="false" selection-start-line="38" selection-start-column="34" selection-end-line="38" selection-end-column="34" />
-          <folding>
-            <element signature="e#68#83#0" expanded="true" />
-          </folding>
-        </state>
-      </provider>
-    </entry>
-    <entry file="file://$PROJECT_DIR$/filter/filter_ref_sites_vcf.py">
+    <entry file="file://$PROJECT_DIR$/genotype/merge_vcf_files.py">
       <provider selected="true" editor-type-id="text-editor">
-        <state relative-caret-position="18">
-          <caret line="11" column="0" lean-forward="false" selection-start-line="11" selection-start-column="0" selection-end-line="11" selection-end-column="0" />
+        <state relative-caret-position="521">
+          <caret line="102" column="34" lean-forward="true" selection-start-line="102" selection-start-column="34" selection-end-line="102" selection-end-column="34" />
           <folding>
-            <element signature="e#154#169#0" expanded="true" />
+            <element signature="e#132#147#0" expanded="true" />
           </folding>
         </state>
       </provider>
diff --git a/scripts/convert/vcf_to_table.py b/scripts/convert/vcf_to_table.py
index 471237003b756491935e6477288a1a1e85b960e5..1bd2bda6a94eb3e043636672e69c10e34c4c9475 100755
--- a/scripts/convert/vcf_to_table.py
+++ b/scripts/convert/vcf_to_table.py
@@ -47,13 +47,15 @@ def vcf_to_table(input_fn, output_fn, fields=None, genotype_fields=None):
         samples = list(vcf.header.samples)
         samples.sort()
         header_fields = []
-        standard_fields = ["CHROM", "POS", "REF", "ALT", "QUAL", "FILTER", "END", "HOM-VAR", "VAR"]
+        standard_fields = ["CHROM", "POS", "REF", "ALT", "QUAL", "FILTER", "END", "HOM-VAR", "VAR", "DEL_SUPPORTED"]
         standard_fields.extend(vcf.header.info)
         if fields:
             for field in fields:
                 if field not in standard_fields:
                     raise ValueError(
                         "{} not defined as standard or INFO field".format(field))
+                if field == "DEL_SUPPORTED":
+                    header_fields.extend(["DEL_SUPPORTED", "DEL_UNSUPPORTED", "NON_DEL_SUPPORTED", "NON_DEL_UNSUPPORTED"])
                 else:
                     header_fields.append(field)
         if genotype_fields:
@@ -116,6 +118,39 @@ def vcf_to_table(input_fn, output_fn, fields=None, genotype_fields=None):
                                 if genotype not in non_variants:
                                     var_calls += 1
                             record_fields.append(str(var_calls))
+                    elif field == "DEL_SUPPORTED":
+                        del_supported_calls = 0
+                        del_unsupported_calls = 0
+                        nondel_supported_calls = 0
+                        nondel_unsupported_calls = 0
+
+                        if record.info["SVTYPE"] != "DEL":
+                            record_fields.extend(["NA", "NA", "NA", "NA"])
+                        else:
+                            for sample in samples:
+                                genotype = record.samples[sample]["GT"]
+                                dhffc = record.samples[sample]["DHFFC"]
+                                non_variants = [(0, 0), (None, None),
+                                                (None, 0)]
+                                if genotype in non_variants:
+                                    if dhffc >= 0.75:
+                                        nondel_supported_calls += 1
+                                    else:
+                                        nondel_unsupported_calls += 1
+                                elif genotype == (0, 1):
+                                    if dhffc >= 0.25 and dhffc < 0.75:
+                                        del_supported_calls += 1
+                                    else:
+                                        del_unsupported_calls += 1
+                                elif genotype == (1, 1):
+                                    if dhffc >= 0 and dhffc < 0.25:
+                                        del_supported_calls += 1
+                                    else:
+                                        del_unsupported_calls += 1
+                            record_fields.append(str(del_supported_calls))
+                            record_fields.append(str(del_unsupported_calls))
+                            record_fields.append(str(nondel_supported_calls))
+                            record_fields.append(str(nondel_unsupported_calls))
                     elif field in record.info:
                         record_fields.append(str(record.info[field]))
                     else:
diff --git a/scripts/genotype/merge_vcf_files.py b/scripts/genotype/merge_vcf_files.py
index 512384745aa6c4fa607a4bb183c5b0b08837e6f8..fccaf9cd87b7ff00c36b73ee479d50a2515faf4f 100755
--- a/scripts/genotype/merge_vcf_files.py
+++ b/scripts/genotype/merge_vcf_files.py
@@ -38,21 +38,23 @@ def parse_cl_args(in_args):
     parser.add_argument("-r", "--reciprocal", type=float, default=0.5,
                         help="Minimum fraction of reciprocal overlap needed "
                              "to collapse calls")
-    parser.add_argument("-he", "--heterozygous", type=bool, default=True,
-                        help="Boolean indicating whether calls will be "
-                             "classified as heterozygozous or homozygous in "
-                             "different samples. "
-                             "All calls will be considered homozygous if false.")
+    parser.add_argument("-he", "--heterozygous", default=False, action='store_true',
+                        help="If set, all heterozygous calls will be considered homozygous.")
+    parser.add_argument("-nge", "--no_genotyping", default=True, action='store_false',
+                        help="If set, calls will not be genotyped based on read depth "
+                             "computations made by duphold.")
     args = parser.parse_args(in_args)
     return args
 
-def obtain_sites_and_genotypes(input_fns, heterozygous=True):
+def obtain_sites_and_genotypes(input_fns, heterozygous=True, genotyping=True):
     """
     Obtain all CNV sites from a list of VCF files
 
     :param input_fns: List of paths to VCF files
     :param heterozygous: Boolean indicating whether calls will be classified
     into heterozygous or homozygous. All calls will be homozygous if false.
+    :param genotyping: Boolean indicating whether calls will be genotyped
+    based on read depth computed by duphold.
     :return: Set containing all sites. Sites are tuples
     (chrom, pos, alt, end, sv_type, inschrom, inspos). Dict containing sites
     as keys and genotype lines of samples as values.
@@ -96,27 +98,44 @@ def obtain_sites_and_genotypes(input_fns, heterozygous=True):
                 dhffc = record.samples[0]["DHFFC"]
                 # set genotypes based on format
                 gt = [".", "."]
-                non_calls = [(None, None), (0, 0)]
+                non_calls = [(".", "."), (0, 0)]
                 called_gt = record.samples[0]["GT"]
-                if not heterozygous:
-                    gt[0] = "1"
-                    gt[1] = "1"
+                if not genotyping:
+                    if called_gt[0] == None:
+                        gt[0] = "."
+                    else:
+                        gt[0] = str(called_gt[0])
+                    if called_gt[1] == None:
+                        gt[1] = "."
+                    else:
+                        gt[1] = str(called_gt[1])
                 else:
                     if sv_type == "INS":
                         # do not call INS if single sample shows reference only or no call
                         if called_gt in non_calls:
-                            gt[0] = called_gt[0]
-                            gt[1] = called_gt[1]
+                            if called_gt[0] == None:
+                                gt[0] = "."
+                            else:
+                                gt[0] = str(called_gt[0])
+                            if called_gt[1] == None:
+                                gt[1] = "."
+                            else:
+                                gt[1] = str(called_gt[1])
                         else: 
                             # call can be only be ./1, based on available evidence
                             gt[1] = "1"                        
                     elif sv_type == "DEL":
+                        print("Wrong")
                         if dhfc >= 0 and dhfc < 0.25:
                             gt[0] = "1"
                             gt[1] = "1"
                         elif dhfc >= 0.25 and dhfc < 0.75:
-                            gt[0] = "0"
-                            gt[1] = "1"
+                            if not heterozygous:
+                                gt[0] = "1"
+                                gt[1] = "1"
+                            else:
+                                gt[0] = "0"
+                                gt[1] = "1"
                         else:
                             gt[0] = "0"
                             gt[1] = "0"
@@ -125,8 +144,12 @@ def obtain_sites_and_genotypes(input_fns, heterozygous=True):
                             gt[0] = "0"
                             gt[1] = "0"
                         elif dhfc >= 1.25 and dhfc < 1.75:
-                            gt[0] = "0"
-                            gt[1] = "1"
+                            if not heterozygous:
+                                gt[0] = "1"
+                                gt[1] = "1"
+                            else:
+                                gt[0] = "0"
+                                gt[1] = "1"
                         else:
                             gt[0] = "1"
                             gt[1] = "1"
@@ -404,7 +427,7 @@ def write_to_output_vcf(output_vcf_fn, chrom_length_dict, sites_interval_trees,
             output_vcf.write("\n")
     return 0
 
-def merge_vcfs(input_fn, output_vcf_fn, chrom_length_dict, reciprocal=0.5, heterozygous=True):
+def merge_vcfs(input_fn, output_vcf_fn, chrom_length_dict, reciprocal=0.5, heterozygous=True, genotyping=True):
     """
     Merge VCF files of single samples containing CNVs called by Hecaton,
     producing a single VCF file containing the merged calls
@@ -414,6 +437,8 @@ def merge_vcfs(input_fn, output_vcf_fn, chrom_length_dict, reciprocal=0.5, heter
     length of chromosomes as values
     :param heterozygous: Boolean indicating whether calls will be classified
     into heterozygous or homozygous. All calls will be homozygous if false.
+    :param genotyping: Boolean indicating whether calls will be genotyped
+    based on read depth computed by duphold.
     :param reciprocal: Minimum reciprocal overlap required to collapse CNVs
     :return: 0 (integer)
     """
@@ -423,7 +448,7 @@ def merge_vcfs(input_fn, output_vcf_fn, chrom_length_dict, reciprocal=0.5, heter
         for line in input_file:
             input_fns.append(line.strip())
     # obtain all sites and genotype information
-    sites_set, samples_dict = obtain_sites_and_genotypes(input_fns, heterozygous)
+    sites_set, samples_dict = obtain_sites_and_genotypes(input_fns, heterozygous, genotyping)
     # get interval tree in which sites considered to be the same CNV are collapsed
     sites_interval_tree = get_interval_tree_from_sites_set(sites_set,
                                                            chrom_length_dict,
@@ -447,7 +472,7 @@ def main():
         raise ValueError("Reciprocal overlap must be between 0 and 1")
     # merge vcf files
     merge_vcfs(args.input_file, args.output_vcf, chrom_length_dict,
-               args.reciprocal, args.heterozygous)
+               args.reciprocal, args.heterozygous, args.no_genotyping)
 
 if __name__ == "__main__":
     main()