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.
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
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.
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