Several reasons motivate us to develop a functional annotation pipeline for genetic variants. First, although companies that manufacture sequencing machines or provide sequencing services typically offer software for functional annotation, these software are usually sequencing platform-specific, and cannot be extended to handle users’ specific needs (such as using different genome builds or gene annotations). Second, although several databases have been developed for the functional annotation of SNPs or CNVs (4–6), most of them are limited to known variants, typically those reported in dbSNP or CNV databases. We note that some exceptions exist (7), for example, the F-SNP tool (8) and Seattle Seq tool (http://gvs.gs.washington.edu/SeattleSeqAnnotation/) can be used for annotation of novel SNPs. Third, several previously developed mutation prediction algorithms, such as SIFT (9) and PolyPhen (10), require building multiple alignments on sequence databases, can only handle non-synonymous mutations, and are difficult to scale up to many model organism genomes. Nevertheless, for human genomes, SIFT/PolyPhen scores for all possible non-synonymous mutations can be computed, so they can be utilized for fast annotation of novel SNVs. Fourth, although it is feasible to
