HGVA aims to provide a high-performance and scalable resource to store, query and visualise variants from main human datasets. We have put special emphasis on making HGVA very responsive even with complex queries and to make the data available to researchers and bioinformaticians in three different ways: a rich web interface based on OpenCB IVA, client libs (Python, Java and JavaScript) and through a command-line. Finally, all data is is normalised and annotated using OpenCB CellBase.

HGVA does not intend to replace or provide the same archiving services of NCBI dbSNP or EMBL-EBI EVA. These archives sites provide an excellent submission and accessioning services and play a crucial role allowing scientist to submit variation data for many different species. On the contrary, we have selected - and we will keep integrating - high-profile studies which are the most widely used in genomic variation analysis pipelines. Big genomic variation repositories such as EVA or dbSNP are multi-species services with a more general archiving aimHGVA is focused on human data only and selects the most relevant and high-quality datasets implementing different rich user interfaces to allow researchers to query all these datasets ar use this information in genomic pipelines.

HGVA is developed and maintained by researchers at University of Cambridge and Genomics England and it is available at http://hgva.opencb.org

Main Features

• Most important high-quality variant studies normalised and integrated in just one server database
• Rich variant annotation performed, including HPO terms, consequence types, substitution effect prediction scores, Gene Ontology terms, etc.
• Population frequencies calculated, including populations and super-populations
• Interactive web-based data mining tool based on IVA
• Clients in Python, Java, JavaScript for fast programmatic access

Contact

• Javier Lopez (javier.lopez@genomicsengland.co.uk)

• Ignacio Medina (im411@cam.ac.uk)