Entering edit mode
5.0 years ago
Nicolas Rosewick
10k
Hi,
Is there a way to extract the allele count for each population of a specific variant using R (oar maybe through a REST API but I couldn't find one for gnomAD..)
For instance I would like to have these informations e.g. for variant https://gnomad.broadinstitute.org/variant/1-55516888-G-GA . I'm interested in the column "Alle Count" and "Allele number".
Thanks
Not API, but maybe this bioconductor package - MafDb.gnomAD.r2.0.1.GRCh38 ?
Or we can always try and scrape the table, maybe see
rvest
.Related post: Extract gnomad AF for specific position with R
varsome has an API, it needs a login, and might not be free.
Is tabix helpful? get in VCF format and use bcftools to extract fields of interest as tsv.
output from GNOMAD vcf is huge (source : https://storage.googleapis.com/gnomad-public/release/2.1.1/vcf/exomes/gnomad.exomes.r2.1.1.sites.vcf.bgz)