This track collection gathers variant allele frequencies from population-scale sequencing and genotyping projects worldwide, from a total of ~1.7 million genomes/exomes/arrays. Unlike gnomAD, the data was not reprocessed in a harmonized way; the variant VCFs were collected from the projects as-is. The goal is a single place to compare how common a variant is across different populations, ancestries, and cohorts, for projects that gnomAD is unlikely to reprocess soon. Three combined tracks aggregate the source data along different lines, and there is also one subtrack per project with the original VCF data and all the annotations that the project provides. The different projects use different pipelines and sequencing technologies. Click any of the projects above or below for a summary of their sample selection, sequencing assay and software pipeline. Many projects do not allow us to distribute the data, but we document how to request it and provide all converters, see Data Download below.

The browser has other tracks with variant frequencies. We have of course the data from gnomAD in separate tracks. Two projects that provide haplotype-phased genotypes can also be found in their own tracks: 1000 Genomes is a separate track, and the phased genotypes HGDP, SGDP, HGDP+1000 Genomes and Mexico Biobank are in the Phased Variants track. Their VCF versions below show only the allele frequency per variant, not the phased genotypes.

Please contact us (genome@soe.ucsc.edu) if you know of a project that we should add. So far, we have requested data from Regeneron's Million Exomes and the Mexico City studies (both requests rejected); Taiwan Biobank and the full UK Biobank WGS data requests are pending.

To view the full description, click here.