Table 2.

Computational aspects of JAM and runtimes (in minutes) of the different methods applied to the meta‐GWAS case studies

Case study	Total	JAM	JAM	JAM	lassosum	LDPred
	SNPs	$\lambda$	SNPs	Runtime	Runtime	Runtime
T1D	231,510	0.01	712	4.6	10.3	61.5
CAD	211,263	0.001	7233	5.1	7.5	27.5
Schizophrenia	385,474	1E‐04	30544	16.6	17.4	157.2

Note: The total number of SNPs analyzed (i.e., after QC), for all methods, is shown in the first column. The next two columns correspond to the optimal value of for use with JAM—smaller values encourage more sparsity—and the posterior average number of SNPs selected into the corresponding optimal JAM model

Abbreviations: CAD, coronary artery disease; SNP, single‐nucleotide polymorphism; T1D, type 1 diabetes.