For region-based annotations, ANNOVAR needs to download annotation databases from the various UCSC Genome Browser tables, based on a user-specified track name. Alternatively, users can specify a custom-built annotation database conforming to Generic Feature Format 3 (GFF3), and ANNOVAR can identify variants overlapping with features annotated in the given GFF3 file. For filter-based annotations, for example, comparing mutations to those detected in the 1000 Genomes Project or dbSNP, ANNOVAR will download specific files from the corresponding websites. ANNOVAR can also download pre-computed SIFT scores for all human non-synonymous mutations, to help annotate human exomes by filter-based annotation procedure.
