HGDP + 1kGP

This repository contains information for QC, analyses, and tutorials relating to the combined HGDP (Human Genome Diversity Project) + 1kGP (1000 Genomes Project) data

Data access

• Metadata available on Google Cloud: gs://gcp-public-data--gnomad/release/3.1/secondary_analyses/hgdp_1kg_v2/metadata_and_qc/gnomad_meta_updated.tsv

  • The metadata can be downloaded from google cloud as described here.

• All data are freely available and described in more detail here.

• The gnomAD HGDP+1kGP callset (pre-QC mt) can be found here.

  • Note that files ending with .bgz can be viewed using zcat on the command line

• Datasets used in the tutorials are located here.

• Phased haplotypes are available as BCFs on Google Cloud: gs://gcp-public-data--gnomad/resources/hgdp_1kg/phased_haplotypes_v2/

  • More details can be found here.

• Datasets found on the Downloads page of the gnomAD browser are released on Google Cloud Platform, Amazon Web Services, and Microsoft Azure. Instructions on how to download them can be found here.

Additional information

PCA plotting and projection scripts available here (used for the COVID-19 Host Genetics Initiative, Global Biobank Meta-analysis Initiative, and related projects to align external cohorts to this resource): https://github.com/atgu/pca_projection/blob/master/hgdp_tgp_reference/hgdp_tgp_pca_intersection.py