Smaller software changes are not announced here. A summary of the three-weekly release changes can be found here. For the full list of our daily code changes head to our GitHub page. Lastly, see our credits page for acknowledgments of the data we host.
-We are pleased to announce a new SNV -Frequencies supertrack on the human assembly (GRCh38/hg38). The +Frequencies container track on the human assembly (GRCh38/hg38). The collection unifies single-nucleotide variant allele frequencies from 30+ population resequencing and biobank projects worldwide, covering roughly 1.7 million genomes, exomes, and genotyping arrays, into a single place where a variant's frequency can be compared across populations, ancestries, and disease cohorts.
The collection includes three combined tracks that aggregate the source data along different lines:
Each variant in the combined tracks is colored by predicted protein consequence (loss-of-function, missense, synonymous, non-coding), and carries pooled allele counts and pooled allele frequencies (sum AC / sum AN) across the contributing cohort arms. Cross-database filters allow you to narrow to variant type, consequence, source database, length, or any combination of per-track AC/AF/AN ranges.
-The supertrack pulls together cohorts from across the world. A high-level +The container track pulls together cohorts from across the world. A high-level summary of the regions and contributing projects is shown below; a complete table with per-cohort sample counts, data types, sub-populations and download status is on the -supertrack -description page. +container +track description page.
| Region | Contributing cohorts |
|---|---|
| East Asia | ToMMo, GenomeAsia, NPM, KOVA, WBBC, ChinaMAP, TPMI |
| South Asia | IndiGen, GenomeIndia |
| Africa | Tishkoff |
| Americas | AllOfUs, TOPMed, ABraOM, Mexico Biobank |
| Europe | FinnGen, SweGen, GoNL, HRC, UK Biobank, ALFA |
| Middle East | Saudi |
| Oceania | MGRB |
| Disease cohorts | SFARI SPARK (WES + WGS), SCHEMA, GREGoR, GA4K |
| Global reference panels | SGDP, gnomAD HGDP+1kG |
| Long-read / linked-read | GA4K, CoLoRSdb, SVatalog |
License restrictions on some sources limit redistribution; see the -supertrack description page for per-cohort details. +container track description page for per-cohort details.
We plan to continue updating this track as more population-scale allele-frequency datasets become available. If you are involved with a project that publishes variant frequencies and would like to contribute, please reach out.
We would like to thank the millions of participants worldwide who donated samples and shared health information to make this data possible; the -investigators who provided the variant files, including Matthew Hansen -(Tishkoff lab), Insoo Jang (KOVA), and Andreas Lahner (MGZ) for feedback; -and Alex Ioannidis (UCSC) for the motivation behind the track. The track -was developed by Maximilian Haeussler with QA and review by Lou Nassar. +investigators and data-access teams who provided the source variant files +and helped shape the track, including Matthew Hansen and Sarah Tishkoff +(Tishkoff lab, Penn) for the Tishkoff180 African cohort, Insu Jang (KOBIC) +for KOVA, Yanan Cao (Shanghai) for ChinaMAP, Matthew Hobbs (Garvan) for +MGRB, Adam Ameur and Johan Viklund for SweGen, Ameena Suliman and Julia +Sommer (SFARI) for SPARK data access, and Cole Shanks and Qudsi Aljabiri +(Ioannidis lab, UCSC) for the All of Us callset; Andreas Lahner (MGZ) for +feedback on the design; and Alex Ioannidis (UCSC) for the motivation +behind the track. The track was developed by Maximilian Haeussler with QA +and review by Lou Nassar.
We are happy to announce release 3 of the Varaico Variants and Varaico Variants (suppl) tracks for the human assemblies hg38/GRCh38 and hg19/GRCh37. This release contains a precision improvement and an update of the underlying literature. The Varaico tracks are created using literature mining, similar to AVADA.