ANNOVAR protocols

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


  • Invertebrates
    • Caenorhabditis elegans
    • Drosophila melanogaster
  • Plants and Fungi
    • Saccharomyces cerevisiae
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus



Add your version


  • person_outline Kai Wang <>

Publications for ANNOVAR

ANNOVAR IN pipelines

PMCID: 5754367
PMID: 29302025
DOI: 10.1038/s41467-017-02306-5

[…] indels were realigned using the genome analysis toolkit (gatk). snvs and short indels were called using gatk haplotype caller (version 3.4–46). all variants were annotated with annovar and in-house scripts, and most likely protein damage variants (nonsense, splice site, frameshift indel, and missense) were considered for further analysis. the variants were also annotated […]

PMCID: 5772158
PMID: 29282330
DOI: 10.1212/WNL.0000000000004820

[…] windows (correction for the number of tests performed in each gene, 0.05/279,713). we performed functional annotations of the snvs with the publicly available variant function predicting software annovar.20 all association analyses were carried out using epacts 3.2.6 software (university of michigan) with the emmax test. finally, we used the meta-analysis gene-set enrichment of variant […]

PMCID: 5780849
PMID: 29363428
DOI: 10.1186/s12864-017-4374-2

[…] 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 […]

PMCID: 5789536
PMID: 29378538
DOI: 10.1186/s12881-018-0527-7

[…] 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: 5792266
PMID: 29217782
DOI: 10.3324/haematol.2017.175810

[…] (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 […]

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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Anonymous user #89

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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.