Extracting MAF for a list of SNPs

Question

[bayoteju]

I have a list of SNPs (about 2000) for which I need their minor allele frequency for EUR. The minor allele frequency is available on dbSNP. How do I automate the extraction of MAF for my SNPs? Doing it one by one would take ages!! Any suggestions?

[finswimmer]

Hello,

what is your understanding of a "minor allel"? The ALT allele? The allele with the lowest frequency (that could be REF as well)? In case of there are several allele under on rs number the second most one?

Furthermore which database are you interested in? 1000 Genomes? gnomAD? ExAC? ...

fin swimmer

Answer 1

[mariamcurbelo2061]

Hi, I'm a newbie in bioinformatics, so sorry if my answer is not the most complete one. I found myself with the similar problem of extracting info from a MAF. I solved it with python panda package. An example will be:

maf_file = panda.read_table("PATH")
filter_maf_file = maf_file.query('name of your column')
filter_maf_file.to_csv("PATH",separate = '\t')

Basically just read the file, filters it, and save it as a coma(tab or enter, or whatever you want) separated file. If you don't know python, I am certain that all programming lenguajes have packages or functions for reading and filtering files, a maf is simply a tab separated file. Hope this helped.