def add_global_af(ht: hl.Table, temp: str) -> hl.Table:
'''
Adds gnomAD global AF annotation to Table
:param Table ht: Input Table
:param str temp: Path to temp bucket (to store intermediary files)
:return: Table with gnomAD global AF annotation
:rtype: Table
'''
# checkpoint table after completing both gnomAD exomes and gnomAD genomes join
temp_path = f'{temp}/join.ht'
ht = ht.checkpoint(temp_path)
# set gnomAD ACs and ANs to 0 if they are missing after the join
ht = ht.transmute(
gnomad_exomes_AC=hl.if_else(hl.is_defined(ht.gnomad_exomes_AC),
ht.gnomad_exomes_AC, 0),
gnomad_genomes_AC=hl.if_else(hl.is_defined(ht.gnomad_genomes_AC),
ht.gnomad_genomes_AC, 0),
gnomad_exomes_AN=hl.if_else(hl.is_defined(ht.gnomad_exomes_AN),
ht.gnomad_exomes_AN, 0),
gnomad_genomes_AN=hl.if_else(hl.is_defined(ht.gnomad_genomes_AN),
ht.gnomad_genomes_AN, 0),
)
ht = ht.annotate(gnomad_global_AF=(
hl.if_else(((ht.gnomad_exomes_AN == 0)
& (ht.gnomad_genomes_AN == 0)), 0.0,
hl.float((ht.gnomad_exomes_AC + ht.gnomad_genomes_AC) /
(ht.gnomad_exomes_AN + ht.gnomad_genomes_AN)))))
ht.describe()
return ht
def join_tables(ht: hl.Table, exomes: bool) -> hl.Table:
'''
Joins seqr variant table to gnomAD table. NOTE code was written assuming most recent gnomAD release is v3
:param Table ht: Table with variants downloaded from seqr
:param bool exomes: Whether to join with gnomAD exomes table or genomes table
:return: seqr variants Table joined with gnomAD table
:rtype: hl.Table
'''
if exomes:
# read in exomes table
gnomad_ht = hl.read_table(
get_gnomad_liftover_data_path('exomes', version='2.1.1'))
gnomad_ht = gnomad_ht.select('freq', 'popmax')
gnomad_ht = gnomad_ht.select_globals()
gnomad_ht = gnomad_ht.transmute(
gnomad_exomes_AC=gnomad_ht.freq[0].AC,
gnomad_exomes_AN=gnomad_ht.freq[0].AN,
gnomad_exomes_popmax_AF=gnomad_ht.popmax[0].AF,
gnomad_exomes_popmax_pop=gnomad_ht.popmax[0].pop)
gnomad_ht.describe()
else:
# read in genomes table
gnomad_ht = hl.read_table(
'gs://gnomad-public/release/3.0/ht/genomes/gnomad.genomes.r3.0.sites.ht'
)
gnomad_ht = gnomad_ht.select('freq')
gnomad_ht = gnomad_ht.transmute(gnomad_genomes_AC=gnomad_ht.freq[0].AC,
gnomad_genomes_AN=gnomad_ht.freq[0].AN)
gnomad_ht = gnomad_ht.select_globals()
gnomad_ht.describe()
ht = ht.annotate(**gnomad_ht[ht.key])
ht.describe()
return ht
