High-throughput sequencing platforms are generating massive amounts of genetic variation data and it remains a challenge to pinpoint the small subset of functionally important variants within an individual genome or cohort of genomes. ANNOVAR™, an efficient command line Perl program to functionally annotate genetic variants from high-throughput sequencing data, was developed to fill this need to shortlist single nucleotide variants and insertions/deletions. Unlike many other annotation programs, ANNOVAR™ works not only with human hg18, hg19 and hg38 genomes but also on diverse genomes such as mouse, worm, fly, yeast and many others.
ANNOVAR™ is widely used for genome annotation by the scientific community, having been downloaded more than 5,000 times and cited in more than 600 scientific publications. ANNOVAR™ is free for academic use, but must be licensed for commercial use. For optimal variant annotation coverage, use ANNOVAR™ in combination with the Genome Trax™ package which includes HGMD® inherited disease mutations, PGMD™ pharmacogenomics variants and TRANSFAC® transcription factor binding sites.