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.
answered Jul 27, 2020 at 13:53
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$\begingroup$ No problem. If you feel like this has answered your question, you can close it by clicking 'accept answer'. $\endgroup$ Jul 30, 2020 at 9:08
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$\begingroup$ Sure thing. When you upvote my question ;-P $\endgroup$ Mar 16, 2022 at 11:16