title: Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR.
abstract: 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.
authors.affiliation: Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California, USA.|Neuroscience Graduate Program, University of Southern California, Los Angeles, California, USA.
authors.forename: Hui
authors.identifier: http://orcid.org/0000-0001-7325-9425
authors.initials: H
authors.lastname: Yang
authors.affiliation: Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California, USA.|Department of Psychiatry, University of Southern California, Los Angeles, California, USA.|Department of Preventive Medicine, Division of Bioinformatics, University of Southern California, Los Angeles, California, USA.
authors.forename: Kai
authors.initials: K
authors.lastname: Wang
mesh_terms: D020022:Genetic Predisposition to Disease; D014644:Genetic Variation; D015894:Genome, Human / Q000235:genetics; D023281:Genomics / Q000379:methods*; D006801:Humans; D058977:Molecular Sequence Annotation / Q000379:methods*; D012984:Software