How to export FinnGen IDs from Atlas

At this time, the Atlas UI does not provide a feature to extract FINNGENIDs from Atlas.

Exporting IDs from Atlas is needed for downstream analysis like GWAS. Exploring new cohorts with tools designed for the purpose is highly recommended before moving to downstream analysis. For further instructions see Cohort Characterizations in Atlas, Cohort Operations tool, Trajectory Visualization tool. See also General workflows for the most common analyses researchers are conducting with the FinnGen data in the Sandbox.

Exporting cohort from Atlas using the Cohort Operation tool

The easiest way to export FinnGen IDs along with other data like birth date, death date, and sex from an Atlas cohort is by using the Cohort Operations tool.

You can also use your Atlas cohorts in the custom GWAS tool.

Step 1:

Custom GWAS tool works so that in UI/Atlas, a user can create a cohort and click “run analysis”.

Step 2:

UI/Atlas will then spit out a phenotype file with IDs and a binary status indicator along with the analysis configuration, which will be automatically picked up for execution without having to go through the current pipelines.

Step 3:

The user will automatically be sent an email when the analysis is ready.