HGDP + 1000 Genomes Ancestry Inference Resource

<strong>Overview</strong> This directory contains a compiled resource between HGDP and 1000G focusing on HapMap3 variants using two deeply sequenced WGS variant callsets (doi:10.1126/science.aay5012, doi:10.1101/2021.02.06.430068) to facilitate an integrated ancestry inference by leveraging both 1000G and HGDP datasets. <strong>Methods</strong> This resource was obtained from the following steps. Downloaded 1000 Genomes WGS genotypes at http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20201028_3202_raw_GT_with_annot/ Downloaded HGDP WGS genotypes at ftp://ngs.sanger.ac.uk/production/hgdp HapMap3 sites were obtained from ftp://share.sph.umich.edu/1000genomes/fullProject/hg38_resources Subset both genotype callsets into HapMap3 sites Merged the genotypes (GT-only) between the callsets on overlapping variants. Split the genotypes into 3433 parents and 698 offsprings and stored into PLINK2 format Performed `cramore vcf-svd` on the parental genotypes (converted to VCF) using cramore (`https://github.com/hyunminkang/cramore with default) parameters so that they can be used for `cramore vcf-infer-ancestry`. Compiled basic metadata information of each sample from HGDP and 1000G. <strong>Available Files</strong> The following files are available in the tarball. README.md : This README file. 1kg_hgdp_hapmap.3way.nochild.autosomes.{pgen,psam,pvar} : Genotypes of 3433 parents on HapMap3 sites 1kg_hgdp_hapmap.3way.child.autosomes.{pgen,psam,pvar} : Genotypes of 698 parents on HapMap3 sites 1kg_hgdp_hapmap.3way.nochild.autosomes.{fUD.gz,V.gz} : Output from `cramore vcf-svd` on 3433 parents. 1kg_hgdp_hapmap.3way.autosomes.sample_metadata.tsv : Sample metadata