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How do I show and/or retrieve variation data from the 1000 Genomes project?

Ensembl contains variation data from the 1000 Genomes project. Currently these are limited to the data from the pilot phase of the project.

To show these data in the browser:

  • Go to the Region in detail page for your region of interest.
  • Click the Configure this page button in the side menu.
  • Click on Germline variation in the pop-up window or alternatively type 1000 genomes in the Find a track text box.
  • Select from the list the 1000 genomes tracks you are interested in.
  • Close the pop-up window.

To retrieve these data genome-wide we recommend using the Perl Variation API. The variations from the 1000 Genomes project are grouped in various variation sets, e.g. 1000 genomes - High coverage - Trios or 1000 genomes - High coverage exons – CEU. All variations within a particular set can be retrieved using the VariationAdaptor method fetch_all_by_VariationSet.

If you have any other questions about Ensembl, please do not hesitate to contact our HelpDesk. You may also like to subscribe to the developers' mailing list.