PAINTOR is an EM-algorithm to jointly fine-map several associated regions by utilizing functional annotation information of individual variants. As a special case of only a single region without annotation information, PAINTOR tackles the standard fine-mapping problem. CAVIAR differs from PAINTOR by modeling the uncertainty in the observed association statistics. This might be a reason why CAVIARBF, a more efficient implementation of CAVIAR, has been reported to be more accurate than PAINTOR in prioritizing variants when no annotation information is available (Chen et al., 2015).
