Python script to collect allele frequency for batch of SNPs in gnomAD database

KalinNonchev / gnomAD_DB

This package scales the huge gnomAD files to a SQLite database, which is easy and fast to query. It extracts from a gnomAD vcf the minor allele frequency for each variant.

MIT License

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Python script to collect allele frequency for batch of SNPs in gnomAD database #30

Closed AR-Shicheng closed 4 months ago

AR-Shicheng commented 4 months ago

Hi Kalin,

Do you think it is a perfect tool to fetch allele frequency data for a batch of SNPs from the gnomAD database, encompassing all populations. Ideally, this script would accept SNP IDs as input and output a data frame containing the allele frequency across different populations, along with the count of homozygous carriers.

https://www.biostars.org/p/9591727/#9591729

Thanks.

Shicheng

KalinNonchev commented 4 months ago

Hi @AR-Shicheng , short answer - yes. Please take a look at the tutorial notebook.