ANNOVAR specifications


Unique identifier OMICS_00165
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Stability Stable
Maintained Yes


  • Animals
    • Caenorhabditis elegans
    • Drosophila melanogaster
    • Homo sapiens
    • Mus musculus
  • Fungi
    • Saccharomyces cerevisiae



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  • person_outline Kai Wang <>

ANNOVAR articles

ANNOVAR citations

PMCID: 5847517

[…] san diego, ca), followed by read alignment using the bwa software, local realignment, base quality recalibration, and variant identification using the gatk software, and variant annotation using annovar22. a 300× average depth of coverage was obtained among variants for the three samples., variants found in lody’s whole blood were divided into those found in the hgmd and those not found […]

PMCID: 5792266

[…] (gatk) best practices. only variants with high-quality reads and a minimum depth of at least 20 and six positives were considered for further analysis. sequencing results were annotated using annovar.24 variants were considered somatic if they were not reported within the exome aggregation consortium (exac) germline database (exac, cambridge, ma, usa). novel splicing, stop-gain […]

PMCID: 5789536

[…] hg19) using the bwa software ( sequence variation annotation was performed using the gatk pipeline ( and annotated using annova (, which comprises gene annotations from multiple sources (including refseq, dbsnp 138, clinvar, and 1000genome)., mutation hotspots in slc12a3 were detected using next […]

PMCID: 5834248

[…] and gatk. variants were called using gatk and followed a best practice procedure implemented at the broad institute [38]., the output mutations in variant call format (vcf) were annotated using annovar [39], which generated an excel-compatible file with gene annotation, amino acid change annotation, dbsnp identifiers [40], and 1000 genomes project allele frequencies [41]., dna was extracted […]

PMCID: 5780849

[…] we used cava [51] (that provides additional clinical information, like disease association, for base variants in human genes) to annotate the a-to-i rna editing sites from human cell lines, and annovar [52] to annotate the rna editing sites from mouse tongue and kidney tissues(cava is not developed to work for mouse genes). sequence pattern around a-to-i rna editing sites in human and mouse […]

ANNOVAR institution(s)
Center for Applied Genomics, Children’s Hospital of Philadelphia, Department of Biostatistics and Epidemiology and Department of Pediatrics, University of Pennsylvania, Philadelphia, PA, USA

ANNOVAR review

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Pierre-Julien VIAILLY's avatar image No country

Pierre-Julien VIAILLY

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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.