Merge pull request #727 from broadinstitute/benb/sex_and_relatedness_bugfixes

Sex and relatedness bugfixes

Author: bpblanken

v03_pipeline/lib/misc/family_loading_failures.py

@@ -22,7 +22,7 @@ def passes_relatedness_check(
     if not coefficients or not np.allclose(
         coefficients,
         relation.coefficients,
-        0.1,
+        atol=0.1,
     ):
         return (
             False,

v03_pipeline/lib/tasks/write_remapped_and_subsetted_callset.py

@@ -118,12 +118,14 @@ def create_table(self) -> hl.MatrixTable:
             relatedness_check_ht = hl.read_table(self.input()[2].path)
             sex_check_ht = hl.read_table(self.input()[3].path)
             families_failed_relatedness_check = get_families_failed_relatedness_check(
-                families,
+                families - families_failed_missing_samples.keys(),
                 relatedness_check_ht,
                 remap_lookup,
             )
             families_failed_sex_check = get_families_failed_sex_check(
-                families,
+                families
+                - families_failed_missing_samples.keys()
+                - families_failed_relatedness_check.keys(),
                 sex_check_ht,
                 remap_lookup,
             )