For each of these three mapping strategies, additional filtering of SNPs based on functional annotations (i.e., CADD, RegulomeDB, and 15-core chromatin state) is optionally available (Methods and Supplementary Table 2). For example, setting a CADD score threshold will cause FUMA to use only highly deleterious SNPs or filtering SNPs by RegulomeDB score or open chromatin state prioritizes SNPs which are likely to affect regulatory elements per one of the mapping strategies.
