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I can't seem to find HGDP data in VCF format.

Does anyone know where I can download it from?

Perhaps there a Snakemake pipeline for calling VCFs from this data?

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I presume you are looking for the recently sequenced WGS data rather than the genotype data? If so, the different files can be found here: ftp://ngs.sanger.ac.uk/production/hgdp/hgdp_wgs.20190516/

Each chromsome has a seperate vcf file with a corresponding .tbi index file.

The gvcfs can be found here: ftp://ngs.sanger.ac.uk/production/hgdp/hgdp_wgs.20190516/gVCFs/

These files are more compressed and smaller in size than the regular vcfs.

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  • $\begingroup$ Fantastic, thanks so much! $\endgroup$ – Dan Bolser Jul 29 '20 at 11:11
  • $\begingroup$ No problem. If you feel like this has answered your question, you can close it by clicking 'accept answer'. $\endgroup$ – user438383 Jul 30 '20 at 9:08

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