Answers.Body: <p>Solution: Use <a href="https://bochet.gcc.biostat.washington.edu/beagle/1000_Genomes_phase3_v5a/b37.vcf/" rel="nofollow noreferrer">https://bochet.gcc.biostat.washington.edu/beagle/1000_Genomes_phase3_v5a/b37.vcf/</a>, then to get the ancestry information (i.e., the ancestry group of each sample, e.g., &quot;HG00566&quot; or &quot;NA19758&quot;) use <a href="https://www.internationalgenome.org/data-portal/sample" rel="nofollow noreferrer">https://www.internationalgenome.org/data-portal/sample</a>.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-05-06T06:29:59.973Z
Answers.LastActivityDate: 2023-05-06T06:29:59.973Z
Answers.UserDisplayName: BigMistake
Answers.Body: <p>For anyone who arrives here looking for a large reference VCF but <em>not</em> wanting GRCh37, you might consider the HGDP+1KG subset of the Genome Aggregation Database's dataset. You can find a VCF file per chromosome aligned, I believe, to GRCh38, <a href="https://gnomad.broadinstitute.org/downloads#v3-hgdp-1kg" rel="nofollow noreferrer">here</a>.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-05-12T15:25:28.617Z
Answers.LastActivityDate: 2023-05-12T15:25:28.617Z
Answers.UserDisplayName: Daniel King
Body: <p>I would like to download a large .vcf file containing many (hundreds or thousands) of samples. Ideally, I would download different population-specific .vcf files, but the ability to sort/filter by ancestry group is fine. Where do I get such a file? I prefer GRCh37 for consistency with other files I'm using.</p>
  <hr />
  <p>Update: I tried the HGDP file--I'm trying the 100 genomes one now, in addition to trying <a href="http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/release/20190312_biallelic_SNV_and_INDEL/" rel="nofollow noreferrer">http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/release/20190312_biallelic_SNV_and_INDEL/</a> now.</p>
  <p>I downloaded the file, but when I opened it it seemed to have no samples (instead of having many samples). Here is a full row:</p>
  <pre><code> 1  10145   .   AAC A   151.43  PASS    AC=4;AF=0.0127389;AN=314;BaseQRankSum=0.72;ClippingRankSum=0;DP=24144;ExcessHet=160.275;FS=0;InbreedingCoeff=-0.1558;MLEAC=5;MLEAF=0.002604;MQ=1.63;MQRankSum=0.764;NEGATIVE_TRAIN_SITE;QD=3.52;ReadPosRankSum=0.085;SOR=0.458;VQSLOD=-0.9391;culprit=QD;VQSRMODE=INDEL;NS=157;ExcHet=0
  </code></pre>
  <p><em>This question has also been asked on <a href="https://www.biostars.org/p/9562337/" rel="nofollow noreferrer">Biostars</a></em></p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-05-03T09:25:28.110Z
Comments.Text: @BigMistake please [edit] your question and give us some context on what you need. You have now mentioned you also need "ancestry information" (which isn't very clear, what kind of information?), and of course you need samples, but please explain all this in your question so we can know what you are after. Ideally, tell us something about how you will use the file so we will be able to give you better answers.
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-09-03T18:56:19.583Z
Comments.Text: Hi @BigMistake thank you for posting your answer. Could you kindly mark this as "accepted"?
Comments.UserDisplayName: M__
Tags: <vcf><genome><1000genomes>
Title: Where do I get a large reference VCF?
ThreadText: # Where do I get a large reference VCF?
  
  (Asked by: username_0 on 2023-05-03)
  
  I would like to download a large .vcf file containing many (hundreds or thousands) of samples. Ideally, I would download different population-specific .vcf files, but the ability to sort/filter by ancestry group is fine. Where do I get such a file? I prefer GRCh37 for consistency with other files I'm using.
  
  ---
  
  Update: I tried the HGDP file--I'm trying the 100 genomes one now, in addition to trying <http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/release/20190312_biallelic_SNV_and_INDEL/> now.
  
  I downloaded the file, but when I opened it it seemed to have no samples (instead of having many samples). Here is a full row:
  
  ```
   1  10145   .   AAC A   151.43  PASS    AC=4;AF=0.0127389;AN=314;BaseQRankSum=0.72;ClippingRankSum=0;DP=24144;ExcessHet=160.275;FS=0;InbreedingCoeff=-0.1558;MLEAC=5;MLEAF=0.002604;MQ=1.63;MQRankSum=0.764;NEGATIVE_TRAIN_SITE;QD=3.52;ReadPosRankSum=0.085;SOR=0.458;VQSLOD=-0.9391;culprit=QD;VQSRMODE=INDEL;NS=157;ExcHet=0
  
  ```
  
  *This question has also been asked on [Biostars](https://www.biostars.org/p/9562337/)*
  
  **Tags:** vcf, genome, 1000genomes
  
  > **Comments:**
  > **username_1**: @username_0 please [edit] your question and give us some context on what you need. You have now mentioned you also need "ancestry information" (which isn't very clear, what kind of information?), and of course you need samples, but please explain all this in your question so we can know what you are after. Ideally, tell us something about how you will use the file so we will be able to give you better answers.  
  > **username_2**: Hi @username_0 thank you for posting your answer. Could you kindly mark this as "accepted"?  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_0 on 2023-05-06. Score: 1 | Accepted answer
  
  Solution: Use <https://bochet.gcc.biostat.washington.edu/beagle/1000_Genomes_phase3_v5a/b37.vcf/>, then to get the ancestry information (i.e., the ancestry group of each sample, e.g., "HG00566" or "NA19758") use <https://www.internationalgenome.org/data-portal/sample>.
  
  
  ---
  
  ### Answer by username_3 on 2023-05-12. Score: 1
  
  For anyone who arrives here looking for a large reference VCF but *not* wanting GRCh37, you might consider the HGDP+1KG subset of the Genome Aggregation Database's dataset. You can find a VCF file per chromosome aligned, I believe, to GRCh38, [here](https://gnomad.broadinstitute.org/downloads#v3-hgdp-1kg).
  
  
  ---
  
  