Command1. This shows the BASH script needed to run a genome-wide analysis. The genotypes and phenotypes are specified with --vcf (line 2) and --bed (line 3), respectively. The analysis is split into 256 non-overlapping chunks (lines 1 and 4) and is based on 1000 permutations (line 5). The full outcome is constructed by concatenating the per-chunk outcomes (line 8).
