The European Variation Archive's third release is out with 1.2 billion variant loci in 227 species

Submitted by marcela.karey on Fri, 02/25/2022 - 09:30
Gramene's collaborators from The European Variation Archive (EVA) Team are delighted to announce the third clustered variants release (RS Release 3) from the EVA consisting of 1.2 billion variant loci in 227 species, including maize (21.4 million new RS ids adding to a total of 79M RS ids), rice (4.9M new RS ids to a total of 15M), sorghum (1M new RS ids to a total of 8.1M), and grapevine (425K RS ids in total). This is the first release where the EVA is publishing all existing variants lifted over to current community reference genome versions. The liftover process has remapped and updated 515 million variants. The main highlights of EVA Release 3 include:
  • Remapping of variants for 37 species to current reference assemblies
  • Release of all variants previously submitted to dbSNP
  • Addition of 345 million variants from 166 studies
More information about the new content in the release can be found at https://www.ebi.ac.uk/eva/?RS-Release&releaseVersion=3.
 
The data from the release is accessible via the following methods:
 
Bulk download
 
The variants are available on the EVA FTP site organized by species/assembly listing all the RS IDs in VCF format. The files include current RS accessioned variants, as well as multi-mapped, deprecated and unmapped variants/IDs. More information regarding the format of the general release can be found in the “README_general_info.txt” and known issues in the release are documented in “README_release_known_issues.txt”.
 
EVA Website
 
Variants can be searched by RS or SS IDs on the EVA website using the SNP search box.
 
REST Interface
 
We provide a comprehensive REST API for programmatic access to all of the EVA data by species, study, and RS ID.We welcome feedback from the community and will aim to incorporate suggestions into future releases. We hope the variants provided are beneficial in future research and the format they are presented in is intuitive.
 
Feedback can be provided using the short survey:
https://tinyurl.com/evarelease3survey
 
For regular updates, please subscribe to EVA's mailing list: https://listserver.ebi.ac.uk/mailman/listinfo/eva-announce
 
On behalf of The EVA Team