We next benchmarked reference-based phasing using either the 1000 Genomes Project Phase 3 reference panel (containing N=2,504 samples from 26 populations)26 or the HRC reference panel r1.1 (containing N=32,470 samples mostly of European ancestry)19. For these benchmarks, we used 1000 Genomes trio children as target samples, removing all 1000 Genomes trios from each reference panel before running the analyses. We phased chromosome 1, and to emulate typical genotyping density, we restricted the SNP set to 31,853 sites typed on 23 and Me (customized Illumina) chips.
