Answers.Body: <p>The best set I'm aware of can be downloaded from <a href="https://gnomad.broadinstitute.org" rel="nofollow noreferrer">https://gnomad.broadinstitute.org</a> .</p>
  
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Answers.Text: Thanks, I have seen there is a Downloads section which hopefully will have the files that I am after.
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Answers.Text: 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?
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Answers.Text: Can you explain what you mean by "population-level?" I see ones for racial and other ethnic groups as well.
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Body: <p>What is the most complete vcf file of population allele frequencies that can be built/downloaded from public datasets nowadays?</p>
  
  <p>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:</p>
  
  <p>CHB CHD MEX GIH TSI LWK ASW MKK HCB JPT CEU YRI</p>
  
  <p>For example, the EnsEMBL project currently has these 12 populations available as a vcf here:</p>
  
  <pre><code>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
  </code></pre>
  
  <p>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.</p>
  
  <p>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 <code>*</code> below:</p>
  
  <pre><code>###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
  </code></pre>
  
  <p>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.</p>
  
  <p>Thanks in advance.</p>
  
Tags: <vcf><genomics><1000genomes><allele-frequency>
Title: what is the most complete vcf file of population allele frequencies that can be built/downloaded from public datasets?
ThreadText: # what is the most complete vcf file of population allele frequencies that can be built/downloaded from public datasets?
  
  (Asked by: username_0 on 2019-06-20)
  
  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.
  
  **Tags:** vcf, genomics, 1000genomes, allele-frequency
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2019-06-20. Score: 4
  
  The best set I'm aware of can be downloaded from <https://gnomad.broadinstitute.org> .
  
  > **Comments:**
  > **username_0**: Thanks, I have seen there is a Downloads section which hopefully will have the files that I am after.  
  > **username_0**: 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?  
  > **username_2**: Can you explain what you mean by "population-level?" I see ones for racial and other ethnic groups as well.  
  
  ---
  
  