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Update liftover #876

Closed
Tracked by #916
, #848
...
nawatts opened this issue Jan 19, 2022 · 1 comment
Closed
Tracked by #916
, #848
...

Update liftover #876

nawatts opened this issue Jan 19, 2022 · 1 comment
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@mattsolo1
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Component: Data Pipeline
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Update browser fo...

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@nawatts
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nawatts commented Jan 19, 2022

Currently, lifted over v2 variants are annotated based on their presence in gnomAD v3.

gnomad-browser/data-pipeline/src/data_pipeline/pipelines/liftover.py

Lines 53 to 60 in 248432d

gnomad_v3_variants = hl.read_table(gnomad_v3_variants_path)
ds = ds.annotate(
datasets=hl.if_else(
hl.is_defined(gnomad_v3_variants[ds.liftover.locus, ds.liftover.alleles]),
ds.datasets.add("gnomad_r3"),
ds.datasets,
)
)

That needs to be updated to use gnomAD v4.
@nawatts nawatts mentioned this issue Jan 19, 2022
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@mattsolo1 mattsolo1 mentioned this issue Jun 23, 2022
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@mattsolo1 mattsolo1 self-assigned this Oct 27, 2023
@mattsolo1 mattsolo1 mentioned this issue Oct 28, 2023
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@mattsolo1
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Closed via #1178

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Update browser for gnomAD v4
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@nawatts @mattsolo1