Version: 2016-12-07 (hg38 lift) Assembly: Human Dec. 2013 (GRCh38/hg38)
Description
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. The
sampling was designed to cover as much anthropological, linguistic and cultural diversity
as possible, so it 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.
Data Access
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.
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 genotyping was performed using GATK
HaplotypeCaller with joint genotyping across all samples. (The Mallick 2016 release also
includes an independent indel callset generated with FermiKit; indels are not carried in
this track.)
The per-sample VCFs were merged with bcftools and lifted to hg38 with CrossMap. At UCSC,
genotypes were stripped to produce a sites-only frequency VCF that keeps the AC, AF, and AN
INFO fields. The deployed file contains 44,756,737 SNV records (601,775 of which represent
multiallelic sites split into separate biallelic records). Indels from the source callset
are not included.
The conversion steps for all source files are documented in the makeDoc file of the track.
Python scripts are also available from GitHub.
Credits
This project was funded by the Simons Foundation. Thanks to David Reich and Swapan
Mallick for help with importing the data.