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

Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR.

Yang H1,2, Wang K1,3,4.

Author information

1
Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California, USA.
2
Neuroscience Graduate Program, University of Southern California, Los Angeles, California, USA.
3
Department of Psychiatry, University of Southern California, Los Angeles, California, USA.
4
Department of Preventive Medicine, Division of Bioinformatics, University of Southern California, Los Angeles, California, USA.

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.

PMID:
26379229
PMCID:
PMC4718734
DOI:
10.1038/nprot.2015.105
[Indexed for MEDLINE]
Free PMC Article

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