Figure 2c-d shows the imputation performance of SNPs and indels respectively when using the CG2 validation set. For this experiment we carried out imputation using genotypes on the Illumina 1M and Omni2.5M chip. We also observe that SHAPEIT2 haplotypes using the 2.5M scaffold produce improved imputation performance compared to the 1000GP Phase 1 set of haplotypes and the Beagle haplotypes, again independently of the sample ancestry (Supplementary Fig. 2). As expected, using a denser chip the imputation improves the results. At 1% frequency SNPs we find that the imputation from the SHAPEIT2 scaffold reference haplotypes into genotypes on the Omni2.5M chip and the Illumina 1M chip produce R2 measures of 0.78 and 0.73 respectively. Interestingly, imputation from the 1000GP Phase 1 set of haplotypes into genotypes on the Omni2.5M chip produces an R2 = 0.73. This highlights the value of using a scaffolded set of haplotypes. In terms of imputation performance, the value of using a scaffold set of haplotypes is equivalent to the use of a much denser SNP chip in the GWAS samples.
