We ran SuSiE 0.7.1.0487 with default values for all parameters except the following: (1) We used 10 causal SNPs per locus; and (2) we estimated a per-locus causal effect size variance (the scaled_prior_variance parameter) via our modified HESS approach. We specified prior causal probabilities via the prior_weights parameter. We modified the SuSiE source code to avoid performing the LD matrix diagnostics (positive-definiteness and symmetry) because they greatly increased memory consumption.
