Code for generating all plots for the paper 'Integration of variant annotations using deep set networks boosts rare variant association genetics' (building on https://github.com/PMBio/deeprvat/)

To run the code, the DeepRVAT conda environment is needed and DeepRVAT has to be installed. Additionaly, the R environment (r-env) should be installed from r-env.yaml.

The UK Biobank genotype and phenotype data required to run all the analyses presented here is not publicly available. We therefore describe for each experiment the required input data/experiment folder set-up in the corresponding README. For detailed information on the input data, the documentation of the DeepRVAT repository should be checked.

Instructions to recreate all main figures and related supplementary figures can be found in the respective figureX directory.

The following environment variables need to be exported when using any pipeline in this repository:

• DEEPRVAT_ANALYSIS_DIR={path_to_this_repository}
• DEEPRVAT_DIR={path_to_the_deeprvat_repository}