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Cancer-Related Analysis of Variants Toolkit CRAVAT

Alternative name: CRAVAT 4 | CRAVAT 5

Performs cancer-related analysis of variants. CRAVAT returns mutation interpretations in a dynamic interactive web environment for sorting, visualizing and inferring mechanism. The software (i) performs all projecting and assigns sequence ontology, (ii) predicts mutation impact using multiple bioinformatics classifiers normalized, (iii) allows for joint prioritization of all non-silent mutation types, organizes annotation from many sources on graphical displays of protein sequence and 3D structure, and (iv) facilitates dynamic filtering. It is suitable for both large and small studies and developed for easy integration with other software.

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CRAVAT classification

CRAVAT specifications

Interface:
Web user interface, Application programming interface
Input data:
Variant calls from sequencing studies in either genomic coordinates (hg18 or hg19) or transcript coordinates—NCBI Refseq, CCDS and Ensembl.
Computer skills:
Basic
Stability:
Stable
Restrictions to use:
None
Input format:
VCF, CRAVAT format
Version:
4.3
Maintained:
Yes

Subtools

  • CHASM (Cancer-specific High-throughput Annotation of Somatic Mutations)
  • VEST
  • SNVGet

CRAVAT distribution

download

CRAVAT support

Maintainer

  • Rachel Karchin <>

Additional information

http://www.cravat.us/CRAVAT/help.jsp?chapter=help_report&article=top

Credits

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Publications

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

Funding source(s)

National Institutes of Health CA 152432; National Science Foundation DBI 0845275

Link to literature

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