Repository to store code for simulations and empirical analyses described in: "Study design and the sampling of deleterious rare variants in biobank-scale datasets." Please see our preprint (here) for details.
Code to produce all figures in the manuscript is available in the figures directory.
We provide code relating to two simulation methods used in the project: branching process simulations (bp_sims) and SLiM simulations (slim_sims). The main simulation file for the branching process method is bp_sims/source/simulations.py. The main simulation file for the SLiM simulations is slim_sims/scripts/rare_variant_simulation.slim.
Scripts pertaining to analysis of UK Biobank WES data can be found in empirical. Scripts for running PCA are available in empirical/pca, while the pipeline for the subsampling experiments can be found in empirical/subsampling_SIR_vF.