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Welcome to HGVA project!

Human Genomic Variation Archive (HGVA) is an open access genomic variation resource that integrates all variants from key world-wide reference projects, but also added-value information such as basic variant annotation, population frequencies, protein effect predictions, variant-associated phenotype, etc.

HGVA is available at http://bioinfodev.hpc.cam.ac.uk/web-apps/hgva

HGVA currently hosts about 400GB of data from 13 different studies describing more than 300 million unique variants. HGVA is not a mere data archive, but a big data provider that enables users to efficiently query, filter and retrieve relevant information from its knowledge-base, either from a visual web-based application or programmatically using RESTful web services.

Main Features

  • Most important high-quality variant studies normalised and integrated in just one server database
  • Rich variant annotation performed
  • Population frequencies calculated
  • Interactive web-based data mining tool based on IVA

Contact

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

  • Ignacio Medina (im411@cam.ac.uk)

Latest news:

HGVA 1.1.0 released!
Javier Lopez posted on Jun 09, 2017
Improved web interface appearance Web interface includes new beta features: Beta Genome Browser available to visualise variant context Summary (beta) tab to get a quick, visual description of filtering result Facets to get graphical descriptions of the data Upgraded backend. HGVA backend is now powered by OpenCGA 1.1.1 Try now! http://hgva.opencb.org http://hgva.opencb.org
HGVA paper published!
Javier Lopez posted on May 30, 2017
HGVA paper has been recently published. Please, cite: Lopez, J., Coll, J., Haimel, M., Kandasamy, S., Tarraga, J., Furio-Tari, P., Rendon, A, Dopazo, J & Medina, I. (2017). HGVA: the Human Genome Variation Archive. Nucleic Acids Research. https://academic.oup.com/nar/article/3848351
gnomAD population frequencies
Javier Lopez posted on May 30, 2017
gnomAD genomes and gnomAD exomes population frequencies are now provided as part of the advanced annotation tab! http://gnomad.broadinstitute.org/


Current Studies

Assembly GRCh37

  • 1000 Genomes Phase 3
  • Exome Aggregation Consortium (ExAC)
  • Exome Sequencing Project (ESP6500)
  • Genome of the Netherlands (GoNL)
  • UK10K project
  • Spanish Medical Genome Project

Assembly GRCh38

  • 1000 Genomes Phase 3

Cancer GRCh37

  • QIMR Berghofer Melanoma
  • Chronic Myeloid Leukemia - Russian Academy of Medical Sciences

Statistics

More than 300M unique variants

1B variants


Developers

Source Code

Web based on IVA project at  https://github.com/opencb/iva/tree/app/hgva

Server based on OpenCGA at  https://github.com/opencb/opencga

Contributing

HGVA is a collaborative project that aims to integrate as many reference human studies as possible, you can contact us for feature request. If you want to contribute to the code you are more than welcome to contribute to IVA and OpenCGA


Recent space activity


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