We evaluated the performance of minimac3 (v1.0.14) in comparison to the three most commonly used imputation tools: minimac2 (v2014.9.15), IMPUTE2 (v2.3.1), and Beagle 4.1 (v22Feb16) (Table 1). We combined chromosome 20 data across multiple whole-genome sequencing studies to generate large reference panels. We compared results for the following seven reference panels: (i) 1000G Phase 1: 1,092 individuals from 1000 Genomes Project Phase 1 (refs. 25,26), (ii) AMD: 2,074 individuals sequenced for study of age-related macular degeneration32, (iii) 1000G Phase 3: 2,504 individuals from 1000 Genomes Project Phase 3 (ref. 1), (iv) SardiNIA: 3,489 individuals from the SardiNIA project4, (v) COMBINED: 9,341 individuals combined together from AMD, SARDINIA, the BRIDGE study of bipolar disorder (L.J.S., unpublished data) (2,464 samples), and the Minnesota Twins study33 (1,314 samples), (vi) Mega: 11,845 individuals obtained by merging COMBINED and G1KP3, and (vii) HRC v1.1: 32,390 individuals from HRC14. To mimic a GWAS, we selected 25 unrelated individuals each from AMD, SardiNIA, BRIDGE Study, and Minnesota Twins and masked all variants except those typed on the Illumina Duo 1M chip (resulting in ~20,000 genotyped variants for
