For calling genotypes in the low coverage samples, the utility of using LD information in addition to sequence data at each site was demonstrated by comparison to genotypes of the exon project, which were derived independently for each site using high coverage data. Fig. 2d shows the SNP genotype error rate as a function of depth at the genotyped sites in CEU. A similar number of variants was called, and at comparable accuracy, using minimum 4x depth in the low coverage project as was obtained with minimum 15x depth in the exon project. To genotype a high fraction of sites both projects needed to make calls at sites with low coverage, and the LD-based calling strategy for the low coverage project used imputation to make calls at nearly 15% more sites with only a modest increase in error rate.
