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European Variation Archive launches

Detailed information about genetic variation is now simpler to explore in the new European Variation Archive (EVA).

European Variation Archive (EVA)
The European Variation Archive launches with data from 15 studies, describing well over one billion submitted variants.

With the launch of its new, open-access European Variation Archive (EVA), EMBL-EBI is making it easier to explore detailed information about genetic variation. The EVA is the first archival resource at EMBL-EBI to provide a single access point for submissions, archiving, and access to high-resolution variation data of all types.

“We are launching the EVA with data from 15 high-profile studies that describe well over one billion submitted variants,” says Justin Paschall, who leads Variation Archives at EMBL-EBI. “It lets you download the data from each study, individually or in bulk, and search it dynamically. That will be a big help to researchers working in this area.”

We are launching the EVA with data from 15 high-profile studies that describe well over one billion submitted variants.

EVA’s 1.7 billion submitted variants are from large-scale efforts including the 1000 Genomes Project, Exome Variant Server, Genome of the Netherlands Project and UK10K.

The data in EVA is linked with external resources including Ensembl to display each variant in its genomic context. You can search the EVA by species, project, chromosomal location and many other fields. It supports complex queries based on gene, study, genomic location and variation type.  It also lets users calculate allele frequencies across submitted studies and populations – a feature unique to EVA.

The submission process is simple: researchers submit a VCF file of their data (and metadata), and the EVA team does the rest. Because the EVA’s workflow is aligned to partner databases in dbSNP, dbVar, and ClinVar, data submitted to EVA is also shared with the National Center for Biotechnology Information (NCBI) in the US, forming the world’s largest open, genetic-variation dataset.

The EVA provides data-mining and visualisation tools for exploring at the level of an individual study or variant. It is deeply linked in underlying read and alignment data available in the European Genome-phenome Archive (EGA) and European Nucleotide Archive European Nucleotide Archive (ENA), so users can follow the evidence chain from sequencing to variant calling.

The EVA is open source, and can be accessed programmatically. We hope our users will test the new EVA to its limits, and welcome all feedback.

This post was originally published on EMBL-EBI News.

Tags: Bioinformatics, Databases, EMBL-EBI, EVA

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