The Simons Genome Diversity Project (SGDP), funded by the Simons Foundation, sequenced high-coverage genomes from 300 individuals (279 in this track) representing 142 diverse and often indigenous populations worldwide. Its goal was to capture the full range of human genetic diversity to better understand population history, migration, and adaptation. It samples populations in a way that represents as much anthropological, linguistic and cultural diversity as possible, and thus includes many deeply divergent human populations that are not well represented in other datasets.
This track shows allele frequencies only. The full phased genotype data with haplotype clustering display is available in the SGDP track under Phased Variants. Not all SGDP data is public, so this track contains only 279 genomes. The hg38 data was lifted from hg19.
The data can be explored interactively with the Table Browser or the Data Integrator. For programmatic access, our REST API can be used; the track name is sgdpFreq. For bulk download, the VCF file can be obtained from our download server.
The original source VCFs are available from https://sharehost.hms.harvard.edu/genetics/reich_lab/sgdp/vcf_variants/.
High-coverage whole-genome sequencing of 300 individuals (279 publicly available) from 142 diverse populations was performed on Illumina instruments using PCR-free library preparation at an average depth of 43x. Reads were aligned to the hs37d5 reference (GRCh37 with decoy sequences) using BWA-MEM 0.7.12. SNP and indel genotyping was performed using GATK HaplotypeCaller with joint genotyping across all samples. An independent indel callset was generated using FermiKit for improved sensitivity at complex variants. The final dataset contains 34.4 million SNPs and 2.1 million short indels.
The VCFs were merged with bcftools and lifted to hg38 with CrossMap. At UCSC, genotypes were stripped to produce a sites-only frequency VCF retaining the existing AC, AF, and AN INFO fields. We provide documentation that indicates how all source files were converted in the makeDoc file of the track. Python scripts are also available from GitHub.
This project was funded by the Simons Foundation. Thanks to David Reich and Swapan Mallick for help with importing the data.
Mallick S, Li H, Lipson M, Mathieson I, Gymrek M, Racimo F, Zhao M, Chennagiri N, Nordenfelt S, Tandon A et al. The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature. 2016 Oct 13;538(7624):201-206. PMID: 27654912; PMC: PMC5161557