How can I download the VCF file of the 1000 genomes project with the population frequencies?
1 answer
The phased VCF files have super-population (AFR, EUR, EAS, ...) allele frequencies (preprint).
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I don't think you can find the 1000 genome VCF file with population frequencies. You have to annotate the VCF yourself using ANNOVAR or VEP, which will add the population frequencies.