Submission quick guide

This is an overview of the submission process. Please read through the steps outlined below before you fill in the submission request form. If you have questions, please write to the FEGA Sweden Helpdesk.

  1. Create a submission request

If you consider FEGA Sweden to be the right place for your data, please fill in the submission request form. The FEGA Sweden Helpdesk will evaluate your request and contact you about the next steps.

  1. Create a user account at EGA

Once your submission request has been accepted, a member of the FEGA Sweden Helpdesk will instruct you on how to create a user account at EGA. This account will enable you to log in to the FEGA Sweden Submitter Portal.

  1. Create a submission

Describe your submission and enter the metadata that can be registered directly in the Submitter Portal.

To learn more about how the Submitter Portal works, click the open book icon in the upper right corner labeled “Take The Tour”. This interactive guide will walk you through the key features and steps involved in submitting data.

  1. Upload data files

Upload the data files to your FEGA Sweden inbox. After the upload is complete, the file names should appear in the Submitter Portal. For more information, please refer to our detailed upload instructions.

  1. Register Runs

Associate each data file with a registered sample and experiment by linking the visible file names to samples and experiments in the Submitter Portal.

  1. Register Analysis

The Analysis should be used exclusively for BAM/BAI, CRAM/CRAI, and VCF files, as well as for linking phenotypes to samples. It serves as a metadata object that connects analysis files to their associated Study, Experiment, and Sample.

  1. Register Dataset(s)

Group your runs/analyses into datasets and link each dataset to a Policy in the Submitter Portal. Data access requests are made at the dataset level, thus, files within a dataset must share the same release conditions. Contact the FEGA Sweden Helpdesk concerning which Policy to link to each dataset.

  1. Finish your submission

Once you have entered all metadata, notify the FEGA Sweden Helpdesk before pressing the ‘Finalize’ button. The Helpdesk will review your submission and contact you if any revisions are required.

  1. Publish the public metadata

All registered studies are automatically placed on hold (‘embargoed’) until the specified release date. On that date, FEGA Sweden will make the relevant public metadata for the submission available through the European Genome-phenome Archive. This does not mean that sensitive data files become openly available. Access to submitted data will still be governed by controlled access procedures.