In comparing chips for GWA studies it has been common to ask what proportion of SNPs not directly genotyped are “captured” or “tagged” by the chip, i.e. are well predicted, via LD, by a SNP, or combination of SNPs, on the chip. To do so it is necessary to define the level of prediction required, or equivalently to set a threshold for the required level of correlation. Although arbitrary, this has often been set at 0.8 [6],[7],[8]. The resulting proportion of SNPs captured at this level is often referred to as the coverage of the chip. Having specified the threshold it is possible to estimate the coverage of a particular chip from HapMap data, although we note that some care is required to account for SNPs not in HapMap [8].
