Creating a User-defined Endpoint(s)

The FinnGen core analysis provides endpoints that cover all branches of the ICD tree. However, there might be specific additional endpoints you are interested in or different definitions of existing endpoints.

We provide a variety of tools you can use to make your own user-defined endpoints. Red data (individual-level data) rights are needed to have access to the tools and data. For more about red data see "What do we mean by "red" and "green" data?", "Do I need "red" or "green" data access?", and "If I already have green data access, how do I apply for red?".

An example workflow may help to choose between the tools, plan your own workflow, and get started with endpoint defining. For instructions of the most common analyses researchers are conducting with FinnGen data in FinnGen Sandbox see General workflows for the most common analyses.

Tools for creating and visualizing a user-defined Endpoint(s) (Tools usage needs red data access).

Tool	Description	GUI tool	coding skills needed
Atlas	Creating user-defined cohorts and visualization	Yes	No
Genome Browser	Examine & export variant-level information	Yes	No
Cohort Operations	Operate cohorts made with other tools (e.g. Atlas, Genotype Browser, R), export cohorts, visualization	Yes	No
TVT	Visualize large numbers of longitudinal cases with glyphs of user-defined conditions, export	Yes	No
RStudio	Interactive coding using R language	No	Yes
Jupyter (Python)	Interactive coding using Python language	No	Yes
Code Snippets	BigQuery connections using R and Python language	No	Yes

For more tools available in the Sandbox see Which tools are available.