Annotate a list of rsIDs with minor allele freq for specific populations
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2.1 years ago
petrstep ▴ 10

Hey everyone!

I need to annotate a list of rsIDs and minor alleles with allele frequencies for specific populations to create a tab-separated list. Below is an example of what I mean on an example of one randomly selected variant.

Columns of the output list being:

ID minor_allele major_allele minor_allele_freq EAS AFR AMR EUR SAS

Example of data:

rs4982708 G A 0.4822 0.1984 0.966 0.389 0.4185 0.2526

Does anybody please know how to do this efficiently and where to get this data from? I know that one can download the entire gnomAD, but I can't imagine how to efficiently search among those huge files contain a vastly higher amount of data than needed for this use-case.

Thanks!

snp gnomad frequency allele dbsnp • 280 views
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