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Remove extreme multiallelic in exomes VDS #580

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Merged
merged 3 commits into from
Mar 18, 2024
Merged

Remove extreme multiallelic in exomes VDS #580

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3de108f
Add option to remove extreme multiallelic in VDS
KoalaQin Mar 12, 2024
383e990
Apply suggestions from code review
KoalaQin Mar 16, 2024
a9bbce3
Small edits
KoalaQin Mar 16, 2024
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9 changes: 9 additions & 0 deletions gnomad_qc/v4/resources/basics.py
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Original file line number Diff line number Diff line change
Expand Up @@ -119,6 +119,15 @@ def get_gnomad_v4_vds(
vds.variant_data._filter_partitions(filter_partitions),
)

# Remove the chr19 site with excessive numbers of alleles (n=27374) which tends to
# create memory issues for `split_multi`.
logger.info("Dropping excessively multi-allelic site at chr19:5787204...")
vds = hl.vds.filter_intervals(
vds,
[hl.parse_locus_interval("chr19:5787204-5787205", reference_genome="GRCh38")],
keep=False,
)

# Count current number of samples in the VDS.
n_samples = vds.variant_data.count_cols()

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