Regarding computational time, the GPA algorithm takes less than 20 minutes to analyze two traits with one annotation data file. The speed of convergence depends on the strength of the GWAS signals. For example, it took about 7 mins and 3 mins to analyze ADHD and SCZ, repectively, as SCZ has stronger GWAS signals than ADHD. For joint analysis of BPD and SCZ, it took about 20 mins. All timings were carried out on a desktop with 3.0 GHz CPU and 16G memory.
