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Update allele frequency data to use gnomAD v4.0 #528

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julesjacobsen opened this issue Nov 3, 2023 · 2 comments
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Update allele frequency data to use gnomAD v4.0 #528

julesjacobsen opened this issue Nov 3, 2023 · 2 comments
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Release 14.0.0
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14.0.0

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@julesjacobsen
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julesjacobsen commented Nov 3, 2023 •
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https://gnomad.broadinstitute.org/news/2023-11-gnomad-v4-0/
https://gnomad.broadinstitute.org/news/2023-11-v4-structural-variants/
https://gnomad.broadinstitute.org/news/2023-11-v4-copy-number-variants/

Can also add in SpliceAI, phyloP and REVEL.
@julesjacobsen julesjacobsen mentioned this issue Nov 13, 2023
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Also use the updated constraint scores

@julesjacobsen julesjacobsen added this to To do in Release 14.0.0 via automation Jan 18, 2024
@julesjacobsen julesjacobsen added this to the 14.0.0 milestone Jan 18, 2024
julesjacobsen added a commit that referenced this issue Jan 25, 2024
@julesjacobsen
Changes for Issue #442, #520, #528
8099fa0 
Massive mega-change updating AlleleParsers to extract AN, AC, HOM from population frequency sources.
Add new Gnomad3 and Gnomad4 AlleleParsers
Add new DirectoryArchive to enable parsing multiple VCF files in a single directory, e.g. for gnomad-v3 and gnomad-v4
Remove dbsnp, exac and esp data sources as these are now merged into gnomad (dbsnp was used as the source of the 1K genomes and TOPMed data).
Update hg19 to use gnomad-v2.1
Update hg38 to use gnomad-v4 (#528)
Update path sources to use dbNSFP v4.5a and include AlphMissense (#520). Remove M-CAP, MPC and PrimateAI
@julesjacobsen julesjacobsen moved this from To do to Done in Release 14.0.0 Jan 29, 2024
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These are included in data release 2402_hg38

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