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
35
stars
10
forks
source link
Python script to collect allele frequency for batch of SNPs in gnomAD database #30
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.
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