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CRAVAT specifications


Unique identifier OMICS_00147
Alternative names Cancer-Related Analysis of Variants Toolkit, CRAVAT 4, CRAVAT 5, Open-CRAVAT
Interface Web user interface, Application programming interface
Restrictions to use None
Input data Variant calls from sequencing studies in either genomic coordinates (hg18 or hg19) or transcript coordinates—NCBI Refseq, CCDS and Ensembl.
Input format VCF, CRAVAT format
Computer skills Basic
Version 4.3
Stability Stable
Maintained Yes


  • CHASM (Cancer-specific High-throughput Annota
  • SNVGet
  • VEST




  • person_outline Rachel Karchin

Additional information An other version is also available, created with the broader variant analysis community :

Publications for Cancer-Related Analysis of Variants Toolkit

CRAVAT citations


Novel putative drivers revealed by targeted exome sequencing of advanced solid tumors

PLoS One
PMCID: 5865730
PMID: 29570743
DOI: 10.1371/journal.pone.0194790
call_split See protocol

[…] enjamini-Hochberg corrected p values, with the null hypothesis positing that the mutation being tested is not functionally related to tumor growth (passenger). The CHASM engine can be accessed at the CRAVAT web site ( Functional Analysis through Hidden Markov Models (FATHMM) algorithm was first developed for the prediction of the functional effects of protein missense vari […]


Mapping genetic variations to three dimensional protein structures to enhance variant interpretation: a proposed framework

Genome Med
PMCID: 5735928
PMID: 29254494
DOI: 10.1186/s13073-017-0509-y

[…] ated to function [].However, the connections between genetic variations and protein structure are not always easy to find. A few computational tools have begun to emerge (cBioPortal [], COSMIC-3D [], CRAVAT [], Jalview [], MuPIT [], MutDB [], STRUM [], Cancer3D []) that enable users to take individual genetic variations, or a list of them, and visualize these in the context of protein structures. […]


High confidence assessment of functional impact of human mitochondrial non synonymous genome variations by APOGEE

PLoS Comput Biol
PMCID: 5501658
PMID: 28640805
DOI: 10.1371/journal.pcbi.1005628

[…] s and classified the variants that exceeded the threshold of 12 as harmful, as suggested by the authors. Variants were submitted to CADD in VCF-like data format. We further retrieved predictions from CRAVAT [], both for mendelian (VEST) [] and cancer (CHASM) [] diseases. Input variants were specified as Ensembl Transcript IDs and amino acid substitutions, using the one-letter encoding. It responde […]


Impact of DNA repair gene polymorphisms on the risk of biochemical recurrence after radiotherapy and overall survival in prostate cancer

PMCID: 5410269
PMID: 28206966
DOI: 10.18632/oncotarget.15282

[…] with the exploitation of dbSNP (, SNPinfo web server (, PolyPhen ( In addition, some tools of CRAVAT ( were used to analyze both genes and polymorphisms. In particular, we defined the possible role of the genetic variants as cancer drivers and we analyzed the canc […]


The Impact of Environmental and Endogenous Damage on Somatic Mutation Load in Human Skin Fibroblasts

PLoS Genet
PMCID: 5082821
PMID: 27788131
DOI: 10.1371/journal.pgen.1006385

[…] e left and right forearms of Donor2 ().Mutations were annotated for their presence within exons and for their functional consequences and potential roles in cancers, using the software Annovar [] and CRAVAT [] (). […]


Computational approaches in target identification and drug discovery

Comput Struct Biotechnol J
PMCID: 4887558
PMID: 27293534
DOI: 10.1016/j.csbj.2016.04.004

[…] data-mining platform aimed at facilitating discovery from genome-wide expression analyses, providing with query and visualization tools for selected or multiple genes across all analyses . The online Cancer-Related Analysis of Variants Toolkit (CRAVAT) can assist the high-throughput assessment and prioritization of genes and missense alterations important for cancer tumorigenesis, by providing pre […]


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CRAVAT institution(s)
Department of Biomedical Engineering, Department of Computer Science, The Institute for Computational Medicine, The Johns Hopkins University, Baltimore, MD, USA; In Silico Solutions, Falls Church, VA, USA; Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
CRAVAT funding source(s)
National Institutes of Health CA 152432; National Science Foundation DBI 0845275

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