The European Variation Archive: A Central Repository for Plant Genetic Variation Data

In collaboration with Gramene and Ensembl Plants, the European Variation Archive (EVA; www.ebi.ac.uk/eva) aims to provide a resource to the plant community that can accession, archive and provide views of genetic variation data more quickly and in a more granular manner than any other resource, worldwide. EVA works with data submitters to archive genetic variation data, in Variant Call Format (VCF) files, to confirm that archived data is truly valid and associated with rich metadata. This ensures that these data are of most benefit to the community and we shall present an overview of this submission process.

At EVA, archived variants are normalized and annotated using a variety of standardized methods, including Ensembl’s Variant Effect Predictor. We shall present the ways in which users can mine these data using filters on the EVA website to construct both study-centric and global queries, filtering on any combination of species, methodology, variant type, phenotype, consequence or allele frequency and show how results from these queries can be downloaded in a variety of formats including VCF and CSV. Additionally, EVA provides a comprehensive RESTful web-service, to allow programmatic access, and hence the integration of these data with other resources (such as Ensembl Plants and Gramene) and this shall also be presented.