def filter(self, mt):
row_filter = mt[self._row_filter].filters if self._row_filter else mt.exclude_row
col_filter = mt[self._col_filter].filters if self._col_filter else mt.exclude_col
pre_filter = row_filter | col_filter
mt = mt.annotate_rows(**{
'hwe_all_aut': hl.struct(
filters=((row_filter == False) &
(hl.agg.filter(((pre_filter == False) &
(mt.hwe_aut == True)),
variant_qc_aggregator(mt).p_value_hwe) < self._hwe_th_all))),
'hwe_all_sex': hl.struct(
filters=((row_filter == False) &
(hl.agg.filter(((pre_filter == False) &
(mt.hwe_sex == True)),
variant_qc_aggregator(mt).p_value_hwe) < self._hwe_th_all)))
})
mt = mt.annotate_rows(**{
'hwe_all': hl.struct(
filters=((hl.agg.any(mt['hwe_all_aut'].filters) == True) |
(hl.agg.any(mt['hwe_all_sex'].filters) == True))
)})
return mt
def filter(self, mt):
col_filter = mt[self._col_filter].filters if self._col_filter else mt.exclude_col
pre_filter = col_filter
mt = mt.annotate_rows(**{
'maf': hl.struct(
filters=hl.agg.filter(pre_filter == False, hl.min(variant_qc_aggregator(mt).AF)) < self._maf_thresh)})
return mt
def filter(self, mt):
col_filter = mt[self._col_filter].filters if self._col_filter else mt.exclude_col
pre_filter = col_filter
mt = mt.annotate_rows(**{
'monomorphic_var': hl.struct(
filters=hl.agg.filter(pre_filter == False, hl.min(variant_qc_aggregator(mt).AC)) == 0)})
return mt
def filter(self, mt):
row_filter = mt[self._row_filter].filters if self._row_filter else mt.exclude_row
col_filter = mt[self._col_filter].filters if self._col_filter else mt.exclude_col
pre_filter = row_filter | col_filter
mt = mt.annotate_rows(**{
'pre_geno_noy': hl.struct(
filters=hl.agg.filter(((pre_filter == False) & (mt.geno_y_excluded == True)),
variant_qc_aggregator(mt).call_rate) < self._pre_geno_cr),
'pre_geno_y': hl.struct(
filters=hl.agg.filter(((pre_filter == False) & (mt.geno_y_only == True)),
variant_qc_aggregator(mt).call_rate) < self._pre_geno_cr)})
mt = mt.annotate_rows(**{
'pre_geno': hl.struct(
filters=((hl.agg.any(mt['pre_geno_noy'].filters) == True) |
(hl.agg.any(mt['pre_geno_y'].filters) == True))
)})
return mt
def filter(self, mt):
row_filter = mt[self._row_filter].filters if self._row_filter else mt.exclude_row
col_filter = mt[self._col_filter].filters if self._col_filter else mt.exclude_col
mt = mt.annotate_rows(cr=hl.or_missing(row_filter == False,
hl.agg.group_by(mt.is_case,
hl.agg.filter(col_filter == False,
variant_qc_aggregator(mt).call_rate))))
mt = mt.annotate_rows(diff=hl.abs(mt.cr[False] - mt.cr[True]))
mt = mt.annotate_rows(**{
'cr_diff': hl.struct(
filters=hl.agg.any((mt.diff > self._cr_thresh) & (mt[self._initial_row_filter].filters == False)))})
return mt
def filter(self, mt):
mt = mt.annotate_rows(variant_qc=variant_qc_aggregator(mt))
row_filter = mt[self._row_filter].filters if self._row_filter else mt.exclude_row
col_filter = mt[self._col_filter].filters if self._col_filter else mt.exclude_col
pre_filter = row_filter | col_filter
mt = mt.annotate_cols(**{
'fstat': hl.struct(
filters=hl.agg.filter(pre_filter == False & mt.locus.in_autosome(),
(hl.agg.inbreeding(mt.GT, hl.min(mt.variant_qc.AF)).f_stat < -self._fhet_th) |
(hl.agg.inbreeding(mt.GT, hl.min(mt.variant_qc.AF)).f_stat > self._fhet_th))
)})
return mt