Obtain MAF column for a summary statistic

I have a summary statistic for which I don’t have a MAF column. I would like to know what is the best way to obtain this information using rs id or CHR:POS:REF: ALT data?

Thanks in advance

Hi @mahantesh19 ,

The minor allele frequency always depends on the studies samples or the population, which was sampled in the GWAS analysis. It means without knowing the source population it is not possible to infer the allele frequencies.

Given you have information on the population, I would recommend to retrieve this information from GnomAD, which provides very reliable data on a wide range of population with a sufficiently large sample size. For a genome-wide lookup, I would highly recommend using hail, for recommended workflows, check out their community page.


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Thanks Daniel. Let me try your suggestion.