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- Caenorhabditis elegans
- Drosophila melanogaster
- Homo sapiens
- Mus musculus
- Saccharomyces cerevisiae
- Kai Wang <>
No open topic.
(Wang et al., 2010)
ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data.
Nucleic Acids Res.
PMID: 20601685 DOI: 10.1093/nar/gkq603
(Yang and Wang, 2015)
Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR.
PMID: 26379229 DOI: 10.1038/nprot.2015.105
(Chang and Wang, 2012)
wANNOVAR: annotating genetic variants for personal genomes via the web.
J Med Genet.
PMID: 22717648 DOI: 10.1136/jmedgenet-2012-100918
Center for Applied Genomics, Children’s Hospital of Philadelphia, Department of Biostatistics and Epidemiology and Department of Pediatrics, University of Pennsylvania, Philadelphia, PA, USA
1 user review
1 user review
ANNOVAR is a very useful Perl package for the annotation of genetic variants detected using NGS. Users can annotate VCF files (or other compatible formats) throw 3 modules :
- Gene-based annotations : identify wether SNPs or CNVs cause protein coding changes using RefSeq, UCSC, ENSEMBL, GENCODE or AceView. Example : “Giving a list of variants in VCF format, what are the genes impacted ?”
- Region-based annotations : identify variants in a specific genomic region. Example : “Giving a list of differentially methylated regions, what are the genes in these loci ?”
- Filter-based annotations : identify variants that are reported in specific databases such as dbNSFP (pathogenicity prediction algorithms), dbSNP, 1000 genomes, ClinVar or COSMIC. Custom databases can be created in GFF format. Example : “Giving a list of variants, how can I find those previously reported as cancer-relevant mutations ?”
Giving a list of VCFs, ANNOVAR produces tab-separated values files which can be easily integrated in bioinformatics pipelines or directly read in a spreadsheet.