< Back to Article

Efficiency and Power as a Function of Sequence Coverage, SNP Array Density, and Imputation

Figure 4

Reduction in errors from joint genotype calls.

(a) To assess the improvement in imputation quality afforded by joint genotype calls with a SNP array (relative to calls based on sequence data alone), we measured sensitivity and specificity at sites absent from the array; errors at these sites can be reduced only through improved imputation. The Metabochip is absent from this plot, as it is not a genome-wide array. Plotted are and , the sum of which equals the number of sites where (1) the gold-standard or called genotype is non-reference and (2) the gold-standard and called genotypes disagree. Normalized values (defined in Materials and Methods) are plotted to show visual trends; actual values are given in Figure S16(b) To assess the reduction in erroneous genotype cluster locations afforded by joint genotype calls with sequence data (relative to calls based on array data alone), we measured sensitivity and specificity at sites on the array. Red bars correspond to and , measured from calls without haplotype phasing; blue bars correspond to and , measured from joint calls. As described in Materials and Methods, these experiments used 82 additional unrelated samples, absent from our other experiments, to inform cluster locations.

doi: https://doi.org/10.1371/journal.pcbi.1002604.g004