We assessed imputation accuracy of 4 different reference panels : 1000 Genomes Phase 3, UK10K, and two versions of the HRC reference panel, with and without re-phasing with SHAPEIT3. To do this we used high-coverage WGS data made publicly available by Complete Genomics (CG) (see URLs). For the pseudo-GWAS samples we used data from 10 CEU samples that also occur in the 1000 Genomes Phase 3 samples. These samples were removed from the various reference panels before using them to assess imputation performance.
