Where do I get a large reference VCF?
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.
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https://www.cog-genomics.org/plink/2.0/resources#phase3_1kg ; you can select the GRCh37 version, and then use plink2 to export VCF(s). The .psam file contains population labels.
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I've previously used https://bochet.gcc.biostat.washington.edu/beagle/1000_Genomes_phase3_v5a/b37.vcf/, but this doesn't appear to contain ancestry information. I know information about the samples ("HG00566" or "NA19758") exists out there somewhere, particularly here: internationalgenome.org/data-portal/sample. You can then filter the samples.