Export FinnGen IDs using CO

Cohort Operations provides the simplest way to export FinnGen IDs. All features of cohorts uploaded to the Cohort Operation tool can then be exported by the tool itself. With CO, we can easily export Atlas cohorts as well as any other cohort loaded on CO or modified using CO.

Alternatively, the FinnGen IDs from an Atlas cohort can also be exported using SuperSet.

The Cohort Operations tool works well together with the Trajectory Visualization tool. Cohorts exported as a text file from CO can be uploaded directly to the TVT.

Downloading a cohort from CO

First, upload your cohort(s) into the Cohort Operation tool. Then, select the cohort you'd like to export (1) and click Download selected cohorts (2).

A Firefox pop-up will prompt you to save the file. If this window doesn't pop up, don't fret - you likely checked "Do this automatically for files like this from now on" during a previous download, and the file will still save to your home directory.

The output file is a tab-separated file, containing the following columns:

COHORT_SOURCE = as.character(NA),
    COHORT_NAME = as.character(NA),
    FINNGENID = as.character(NA),
    COHORT_START_DATE = lubridate::as_date(NA),
    COHORT_END_DATE = lubridate::as_date(NA),
    SEX = as.character(NA),
    BIRTH_DATE = lubridate::as_date(NA),
    DEATH_DATE = lubridate::as_date(NA)

Therefore, if you're only interested in the FinnGen IDs of your cohort, simply save the third column in the software of your choice.

See also a tutorial video about CO available from FinnGen data users meeting 25th Jan 2022 recording at 16min35sec and FinnGen data users' meeting 28th June 2022 at 28min55sec.