Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR

Nat Protoc. 2015 Oct;10(10):1556-66. doi: 10.1038/nprot.2015.105. Epub 2015 Sep 17.


Recent developments in sequencing techniques have enabled rapid and high-throughput generation of sequence data, democratizing the ability to compile information on large amounts of genetic variations in individual laboratories. However, there is a growing gap between the generation of raw sequencing data and the extraction of meaningful biological information. Here, we describe a protocol to use the ANNOVAR (ANNOtate VARiation) software to facilitate fast and easy variant annotations, including gene-based, region-based and filter-based annotations on a variant call format (VCF) file generated from human genomes. We further describe a protocol for gene-based annotation of a newly sequenced nonhuman species. Finally, we describe how to use a user-friendly and easily accessible web server called wANNOVAR to prioritize candidate genes for a Mendelian disease. The variant annotation protocols take 5-30 min of computer time, depending on the size of the variant file, and 5-10 min of hands-on time. In summary, through the command-line tool and the web server, these protocols provide a convenient means to analyze genetic variants generated in humans and other species.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Genetic Predisposition to Disease
  • Genetic Variation*
  • Genome, Human / genetics
  • Genomics / methods*
  • Humans
  • Molecular Sequence Annotation / methods*
  • Software*