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?
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.