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.