Hello, Does anyone knows how to download or get only snp from hapmap EUR population for gtex v8 models? I tried to get the snp annotation file from gtex portal and downloaded the lookup table in order to get the snp_annotation file. Thank you.
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written
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rheab1230 •
1 answer
Hi Rheab,
Yes, certainly! First, for JUST hapmap, go to hapmap's FTP site.
One thing, though. Nowadays, there are more comprehensive options out there. Two that I recommend, for various reasons, are:
Check out Ensembl VEP. Steps: click link, paste in an rsID > run job > once job is finished, you will see a table in your browser. You can download this, including columns broken out by global MAF, then MAF for each ancestry specifically. Example result for a variant I just ran.
If you want to take a deeper dive into a confined genomic locus (max 50,000bp in length) then Kaviar is a good option. This database contains more variants than dbSNP, even, and includes allele fractions down to very low percentages.
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