Merge pull request #185 from dvitale199/related

updated het to +/-0.15
dvitale199 · Jun 20, 2024 · 6fbea97 · 6fbea97
2 parents b72113c + 9c4dba2
commit 6fbea97
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diff --git a/genotools/__main__.py b/genotools/__main__.py
@@ -64,7 +64,7 @@ def handle_main():
 
     if args_dict['het'] is not None:
         if len(args_dict['het']) == 0:
-            args_dict['het'] = [-0.25, 0.25]
+            args_dict['het'] = [-0.15, 0.15]
 
         else:
             args_dict['het'] = [float(i) for i in args_dict['sex']]
@@ -81,7 +81,7 @@ def handle_main():
         args_dict['callrate'] = 0.05
         args_dict['sex'] = [0.25, 0.75]
         args_dict['related'] = True
-        args_dict['het'] = [-0.25, 0.25]
+        args_dict['het'] = [-0.15, 0.15]
 
     if args_dict['all_variant']:
         args_dict['geno'] = 0.05

diff --git a/genotools/qc.py b/genotools/qc.py
@@ -244,7 +244,7 @@ def run_sex_prune(self, check_sex=[0.25,0.75]):
         return out_dict
 
 
-    def run_het_prune(self, het_filter=[-0.25,0.25]):
+    def run_het_prune(self, het_filter=[-0.15,0.15]):
 
         """
         Execute heterozygosity-based pruning on genotype data using PLINK.