ANNOVAR statistics

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Protocols

ANNOVAR specifications

Information


Unique identifier OMICS_00165
Name ANNOVAR
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

Taxon


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

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Versioning


No version available

Maintainer


  • person_outline Kai Wang

Publications for ANNOVAR

ANNOVAR citations

 (1099)
call_split

Molecular, Pathological, Radiological, and Immune Profiling of Non brainstem Pediatric High Grade Glioma from the HERBY Phase II Randomized Trial

2018
Cancer Cell
PMCID: 5956280
PMID: 29763623
DOI: 10.1016/j.ccell.2018.04.004
call_split See protocol

[…] gatk/). Somatic variants were covered by at least 20 reads in both tumor and normal sequences and carried at least 5 ALT reads in the tumor sequence; unmatched exomes (n=3) were annotated by ExAc and ANNOVAR. Variants were annotated using the Ensembl Variant Effect Predictor v74 (ensembl.org/info/docs/variation/vep) incorporating SIFT (sift.jcvi.org) and PolyPhen (genetics.bwh.harvard.edu/pph2) pr […]

library_books

Outlier response to anti PD1 in uveal melanoma reveals germline MBD4 mutations in hypermutated tumors

2018
Nat Commun
PMCID: 5951831
PMID: 29760383
DOI: 10.1038/s41467-018-04322-5

[…] .php; MuTect2, https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_cancer_m2_MuTect2.php; SAMtools mpileup, http://samtools.sourceforge.net/; ANNOVAR, http://annovar.openbioinformatics.org/en/latest/; cosmic80, cancer.sanger.ac.uk; GDC portal, https://portal.gdc.cancer.gov; ExAC database, http://exac.broadinstitute.org/; cbioportal, http:// […]

library_books

Genomic features of renal cell carcinoma with venous tumor thrombus

2018
Sci Rep
PMCID: 5945671
PMID: 29748622
DOI: 10.1038/s41598-018-25544-z

[…] ased variants were filtered out. Somatic SNVs were called functional, when they were nonsynonymous, occurred within splice sites, or lead to gain or loss of stop codons. All SNVs were annotated using Annovar (version as of February 2016), dbSNP (build 147), 1000 Genomes and EVS (Exome Variant Server, NHLBI GO Exome Sequencing Project (ESP), Seattle, WA [version ESP6500SI-V2]) data. Indels were ide […]

library_books

Genetic analyses in a cohort of 191 pulmonary arterial hypertension patients

2018
PMCID: 5944100
PMID: 29743074
DOI: 10.1186/s12931-018-0789-9

[…] rd software. SNPs and insertions/deletions were identified using the GATK HaplotypeCaller program (http://www.broadinstitute.org/gsa/wiki/index.php/Home_Page) and further annotated with comprehensive ANNOVAR software for their frequencies in the Genome Aggregation Database (gnomAD) for the pathogenicity and splicing-altering prediction of single nucleotide variants in the dbNSFP database, which in […]

library_books

Mutation analysis of SLC26A4 (Pendrin) gene in a Brazilian sample of hearing impaired subjects

2018
BMC Med Genet
PMCID: 5941635
PMID: 29739340
DOI: 10.1186/s12881-018-0585-x

[…] he steps of BAM processing (realignment based upon known local indels and variant quality score recalibration), and variant call (with Unified Genotyper). Variants in the VCF file were annotated with Annovar []. Variant frequencies were compared to the 1000 genomes (http://www.1000genomes.org), ESP6500 (http://evs.gs.washington.edu/EVS/), 65000 exomes from Exome Aggregation Consortium (ExAC) (http […]

library_books

Mutation of IPO13 causes recessive ocular coloboma, microphthalmia, and cataract

2018
PMCID: 5938035
PMID: 29700284
DOI: 10.1038/s12276-018-0079-0

[…] hg19 human genome. Single-nucleotide variants and insertion–deletion variants were identified by GATK (https://software.broadinstitute.org/gatk/). The variants were annotated across the genome using ANNOVAR (www.openbioinformatics.org/annovar/). We performed genome-wide homozygosity mapping using HomozygosityMapper (http://www.homozygositymapper.org/) based on the variant call format (VCF) file o […]

Citations

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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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Desktop
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.