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Download or create VCF from Human Genome Diversity Project (HGDP)

Bioinformatics Asked on September 26, 2021

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?

One Answer

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 by user438383 on September 26, 2021

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