I have more than 800 snps with rs ids, i want to calculate the allele frequency of these snps in British (GBR) population from 1000 Genomes Project. The thing is that i can calculate the allele frequencies of super population like European (EUR) using VEP script but unable to find the way to calculate the allele frequency of specific population like British (GBR) population.
Thank you, got the answer
Installation of Ensembl Rest API on R:
Install latest Rtools in base R from: https://cran.r-project.org/bin/windows/Rtools/
R code for Ensembl Rest API:
Dear Emily, your post above helped us a lot! Two questions: 1) The reported MAF in the JSON is always based on 1000Genomes? 2) Is there some other database providing sub-population resolution in addition to 1000Genomes?
Overall MAF is always 1000 Genomes, but if you get population MAFs they will come from different sources and will be labelled with their source.