We downloaded the GLs for 1,092 1000GP samples from ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/. This dataset contains GLs for 36,820,992 SNPs, 1,384,273 short bi-allelic indels and 14,017 structural variations (SVs). The GLs for SNPs were computed using SNPtools [15], for Indels using [16] and SVs using [17]. We ran Beagle and SHAPEIT2 on the whole genome in chunks of 1.4 Mb with a 0.2 Mb overlaps between flanking chunks.
