VAT statistics

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Associated diseases

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VAT specifications


Unique identifier OMICS_04075
Name VAT
Alternative name Variant Annotation Tool
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Output format VCF
Operating system Unix/Linux
Programming languages C, PHP
Parallelization MapReduce
Computer skills Advanced
Version 2.0.1
Stability Stable
GNU Scientific Library, GD library, Tabix, BlatSuite, BIOS library
Source code URL
High performance computing Yes
Maintained Yes


  • Primates
    • Homo sapiens



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  • person_outline Mark Gerstein <>
  • person_outline Lukas Habegger <>

Publication for Variant Annotation Tool

VAT in publications

PMCID: 5309843
PMID: 28181519
DOI: 10.1038/ncomms14458

[…] was sequenced in more than 80% of accessions. sites with indels, more than two alleles, or more than 10% missing data were further excluded. snps were classified as synonymous or non-synonymous by variant annotation tool v.2.0.1 (ref. ). relicts were identified with the same method as before: the median distance of each accession to all others was calculated, and relicts were defined […]

PMCID: 5192301
PMID: 28070503
DOI: 10.1155/2016/7983236

[…] other vcf annotation tools are snpeff [] and snpsift []. snpeff can perform annotation for multiple variants and snpsift allows rapid detection of significant variants from the vcf files []. the variant annotation tool (vat) distinguishes itself from other annotation tools in one aspect by adding cloud computing capabilities []. vat annotation occurs at the transcript level to determine […]

PMCID: 3907911
PMID: 24498629
DOI: 10.1002/mgg3.42

[…] in total, combining data obtained with the two approaches, we identified 25,516 novel single-nucleotide polymorphisms (snps) and 9144 novel indels (fig.  and s1). we annotated our vcf files using variant annotation tool version 2.0.1 (habegger et al. ). for this analysis we focused on lof variants, considering the importance of their likely biological consequences as well as their increased […]

PMCID: 3618277
PMID: 23577066
DOI: 10.1371/journal.pone.0059494

[…] relaxation of purifying selection, and/or an increased mutation rate , ., p-values were computed for significance of enrichment by gorilla (, using the variant annotation tool (version 2.0.1.) with the gencode v7 annotation , we examined snps and indels for variants predicted to result in the complete loss-of-function (lof). lof variants […]

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VAT institution(s)
Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Department of Computer Science, Yale University, New Haven, CT, USA; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, USA; Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY, USA; Department of Chemistry, Yale University, New Haven, CT, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
VAT funding source(s)
Supported by the National Institutes of Health.

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