The field of complex trait genetics is moving rapidly towards an understanding that deep re-sequencing technologies will provide the necessary data to unearth novel-associated loci. It is anticipated that researchers will soon be faced with the challenge of selecting the appropriate analytical strategy for these data sets, which will be of unprecedented scale and depth. In this study, we have developed and evaluated targeted rare variant analysis methods and have provided insights into their relative merits. The methodology we have developed here for detecting rare variant associations is extremely simplistic, and as technologies probing human genome sequence variation move rapidly forward, the development and testing of analytical strategies that maximise output from these investments will continue to be of critical importance.
