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What is the most complete vcf file of population allele frequencies that can be built/downloaded from public datasets nowadays?

About 5 years or so ago, it used to be the latest release of the CSHL HapMap 12 populations that were part of the 1000 genomes project. These were:

CHB CHD MEX GIH TSI LWK ASW MKK HCB JPT CEU YRI

For example, the EnsEMBL project currently has these 12 populations available as a vcf here:

http://ftp.ensembl.org/pub/current_variation/vcf/homo_sapiens/

CSHL-HAPMAP-HAPMAP-CHB.vcf.gz
CSHL-HAPMAP-HAPMAP-CHD.vcf.gz
CSHL-HAPMAP-HAPMAP-MEX.vcf.gz
CSHL-HAPMAP-HAPMAP-GIH.vcf.gz
CSHL-HAPMAP-HAPMAP-TSI.vcf.gz
CSHL-HAPMAP-HAPMAP-LWK.vcf.gz
CSHL-HAPMAP-HAPMAP-ASW.vcf.gz
CSHL-HAPMAP-HAPMAP-MKK.vcf.gz
CSHL-HAPMAP-HapMap-HCB.vcf.gz
CSHL-HAPMAP-HapMap-JPT.vcf.gz
CSHL-HAPMAP-HapMap-CEU.vcf.gz
CSHL-HAPMAP-HapMap-YRI.vcf.gz

Each SNP has an AF entry from which a multi-populations vcf with rsids, alleles and frequencies can be built, where the AFs are such as AF_CHB, AF_CHD, etc.

The 1000 genomes project populations documentation describes more than these 12 populations, but I haven't seen equivalent population vcfs with AFs built from the individuals within the population for the remainder of these, apart from the original HapMap 12 marked with a * below:

###Populations and codes

*         CHB   Han Chinese             Han Chinese in Beijing, China
*         JPT   Japanese                Japanese in Tokyo, Japan
         CHS    Southern Han Chinese    Han Chinese South
         CDX    Dai Chinese             Chinese Dai in Xishuangbanna, China
         KHV    Kinh Vietnamese         Kinh in Ho Chi Minh City, Vietnam
*         CHD   Denver Chinese          Chinese in Denver, Colorado (pilot 3 only)

         CEU    CEPH                    Utah residents (CEPH) with Northern and Western European ancestry 
*         TSI   Tuscan                  Toscani in Italia 
         GBR    British                 British in England and Scotland 
         FIN    Finnish                 Finnish in Finland 
         IBS    Spanish                 Iberian populations in Spain 

*         YRI   Yoruba                  Yoruba in Ibadan, Nigeria
*        LWK    Luhya                   Luhya in Webuye, Kenya
         GWD    Gambian                 Gambian in Western Division, The Gambia 
         MSL    Mende                   Mende in Sierra Leone
         ESN    Esan                    Esan in Nigeria

*         ASW   African-American SW     African Ancestry in Southwest US  
         ACB    African-Caribbean       African Caribbean in Barbados
         MXL    Mexican-American        Mexican Ancestry in Los Angeles, California
         PUR    Puerto Rican            Puerto Rican in Puerto Rico
         CLM    Colombian               Colombian in Medellin, Colombia
         PEL    Peruvian                Peruvian in Lima, Peru

*         GIH   Gujarati                Gujarati Indian in Houston, TX
         PJL    Punjabi                 Punjabi in Lahore, Pakistan
         BEB    Bengali                 Bengali in Bangladesh
         STU    Sri Lankan              Sri Lankan Tamil in the UK
         ITU    Indian                  Indian Telugu in the UK

I presume there is more public data nowadays that can be accessed to build a more complete vcf files of allele frequencies per population, with as many populations as possible to use as a reference dataset with new data.

Thanks in advance.

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The best set I'm aware of can be downloaded from https://gnomad.broadinstitute.org .

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  • $\begingroup$ Thanks, I have seen there is a Downloads section which hopefully will have the files that I am after. $\endgroup$
    – 719016
    Jun 21, 2019 at 9:09
  • $\begingroup$ I could only find continent-level AFs for gnomAD. I presume nobody built the population-level frequencies file for these individuals, but maybe someone did and this is available on a website? $\endgroup$
    – 719016
    Jun 24, 2019 at 7:36
  • $\begingroup$ Can you explain what you mean by "population-level?" I see ones for racial and other ethnic groups as well. $\endgroup$
    – abalter
    Feb 1, 2021 at 22:38

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