Resources for finding out the allele frequency of a SNV by subpopulation
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4.4 years ago
Vincent Laufer ★ 1.4k

Several biostars posts, for example How To Calculate A Population Specific Allele Freq In 1000 Genomes Release 20101123 Using Vcftools? Getting Population Specific Allele Frequency For Illumina Genotyping Data and Population Level Allele Frequencies For The 1000 Genomes 20101123 Release, among others, have addressed the question of how to get allele frequency of a genetic variant such as a SNP.

Data from the 1000 genomes project may be obtained from VEP, from dbSNP, or from 1kG itself. At this time, I am looking for additional sources of genetic data. I looked through Hapmap phase II and III, neither had this variant.

In particular, I am interested in the MAF of this variant in persons of Yoruban and African American descent. Are there any reference databases containing a large amount of YRI or ASW genetic data that I could use to get more accurate estimates than from 1kG?

Thank you very much.

SNP Allele Frequency MAF subpopulation • 1.1k views
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