We evaluated the computational cost of each method. SuSiE and PolyFun + SuSiE were much faster than the other methods, fine-mapping a 3Mb locus in 5 minutes on average (excluding fixed preprocessing time; see below) (Figure 1e, Supplementary Table 4). CAVIARBF methods allowing >2 causal SNPs per locus were not evaluated due to prohibitively slow computation time. PolyFun also requires fixed preprocessing time (steps 1–4; see Overview of methods) of 630 minutes on average; when restricting analyses to subsets of loci, PolyFun + SuSiE was still faster than all other functionally-informed methods when analyzing >23 loci (Figure 1f).
