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CRAVAT - Cancer-Related Analysis of Variants Toolkit

By Rachel Karchin1, Michael C Ryan2

1. Johns Hopkins University 2. In Silico Solutions

Published on


cravat is a bioinformatics pipeline : ; that performs high-throughput cancer-related analysis of variants. it : ; utilizes three applications: CHASM (Cancer-Specific Analysis of Somatic Mutations), VEST and SVN-Get. More information on these tools is available at CHASM Software.

Release Notes:

May 12, 2015

  • Added RESTful API for annotating a single mutation.
  • Added analytical p-values for VEST pathogenicity scores for non-silent mutations.
  • Added gene-level p-value and FDR for VEST pathogenicity score based on Stouffer's Z-score method
  • Added indel scores.
  • Added mutation allele frequencies from Exome Aggregation Consortium (ExAC) release 0.3.
  • Added input line number to the report.
  • Added a report tab for non-coding mutations.
  • Added a report tab for errorneous input lines.
  • Removed the Codon Level report tab.
  • CRAVAT can now show both driver (CHASM) and pathogenicity (VEST) scores at the same time.
  • Updated VCF support (sequencing quality metrics, zygosity, and pileup coverage and allele frequency).
  • Updated 1000 genomes annotation with Phase3 sequence freeze 20130502 (Includes chromosome Y variants).
  • Updated ESP6500 annotation with version v0.0.30 (Includes chromosome Y variants).
  • Updated GeneCards summary annotation.
  • Updated MuPIT link out according to the new release of MuPIT Interactive.
  • Improved report layout.
  • Improved speed with pre-computation of VEST scores for all possible exome mutations.
  • Fixed bugs.

Overview & Tutorials

Learn more about the utility and value of this open source bioinformatics application at CRAVAT Introduction Video - Cancer Related Analysis of Variants


Dr. Rachel Karchin Associate Professor, The William R. Brody Faculty Scholar, Johns Hopkins University. Institute for Computational Medicine, Department of Biomedical Engineering, Department of Oncology.




Carter H, Chen S, Isik L, Tyekucheva S, Velculescu VE, Kinzler KW, Vogelstein B, Karchin R (2009) Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations Cancer Res, 69(16):6660-7.

Carter H, Douville C, Stenson P, Cooper D, Karchin R (2013) Identifying Mendelian disease genes with the Variant Effect Scoring Tool BMC Genomics, 14(Suppl 3):S3.

Wong WC, Kim D, Carter H, Diekhans M, Ryan M, Karchin R (2011). CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer Bioinformatics, 27(15):2147-2148.


Douville C, Carter H, Kim R, Niknafs N, Diekhans M, Stenson PD, Cooper DN, Ryan M, Karchin R (2013). CRAVAT: Cancer-Related Analysis of Variants Toolkit Bioinformatics, 29(5):647-648.

Cite this work

Researchers should cite this work as follows:

  • Rachel Karchin; Michael C Ryan (2015), "CRAVAT - Cancer-Related Analysis of Variants Toolkit,"

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