In addition to considering only causal configurations with up to three SNPs under scenario A, we also ran FINEMAP with K = 5 to demonstrate the increase in fine-mapping performance in this case where the true number of causal SNPs was five. We determined the proportion of causal SNPs that are included when selecting different numbers of top SNPs on the basis of ranked single-SNP inclusion probabilities (Fig. 5). FINEMAP and CAVIARBF had the same performance when considering causal configurations with up to three SNPs in genomic regions with 1500 SNPs. (Similar performance was also observed for genomic regions with different numbers of SNPs.) As expected, FINEMAP showed better fine-mapping performance when considering causal configurations with up to five SNPs.
