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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

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    $\begingroup$ @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. $\endgroup$
    – terdon
    May 3, 2023 at 9:25
  • $\begingroup$ Hi @BigMistake thank you for posting your answer. Could you kindly mark this as "accepted"? $\endgroup$
    – M__
    Sep 3, 2023 at 18:56

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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.

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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.

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