While reading variants from input file, ANNOVAR scans the gene annotation database stored at local disk, and identifies intronic variants, exonic variants, intergenic variants, 5′/3′-UTR variants, splicing site variants and upstream/downstream variants (less than a threshold away from a transcript, by default 1 kb). For intergenic variants, the closest two genes and the distances to them are reported. For exonic variants, ANNOVAR scans annotated mRNA sequences to identify and report amino acid changes, as well as stop-gain or stop-loss mutations. ANNOVAR can also perform region-based annotations on many types of annotation tracks, such as the most conserved elements and the predicted transcription factor binding sites. These annotations must be downloaded by ANNOVAR, before they can be utilized. Finally, ANNOVAR can filter specific variants such as SNPs with >1% frequency in the 1000 Genomes Project, or non-synonymous SNPs with SIFT scores >0.05.
