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.
At a glance
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- Supplementary Figure 1: The expected results for discovering candidate genes of the ‘hemolytic anemia’ example in the Phenolyzer website. (96 KB)
Each ball represents one of the top 50 ranked genes. The larger the ball, the higher the ranking. The blue balls represent disease genes reported before and the yellow ones represent predicted disease genes. For detailed explanations on each color and shape, and on how the algorithm works to find disease genes, please visit http://phenolyzer.usc.edu/FAQ.php
- Supplementary Figure 2: Explanation of each column in the wANNOVAR web view. (281 KB)
This is a sample output with default parameters. The first 5 columns represent the original information on the input variants. The following 5 columns give gene-based annotations on each variant. The following columns give region-based and filter-based annotations on each variant.
- Supplementary Text and Figures (861 KB)
Supplementary Figures 1 and 2, Supplementary Tables 1–3
- Supplementary Data (464 KB)
ANNOVAR and VEP comparison results