What it does
CRAVAT: Cancer-Related Analysis of VAriants Toolkit is a web server with simple interface where cancer-related analysis of variants are performed. To cite CRAVAT, please use this article.
CRAVAT currently employs three analysis tools, CHASM, SNVGet, and VEST
Input
-Comment lines start with ">", "#", or "!".
-Data fields are separated by a tab or a space.
-The following two formats can be used for input data, but all the data rows should be in the same format:
Genomic-coordinate format (separated by a tab or a space):
# UID / Chr. / Position / Strand / Ref. base / Alt. base / Sample ID (optional) TR1 chr17 7577506 - G T TCGA-02-0231
TR2 chr10 123279680 - G A TCGA-02-3512
TR3 chr13 49033967 + C A TCGA-02-3532
TR4 chr7 116417505 + G T TCGA-02-1523
TR5 chr7 140453136 - T A TCGA-02-0023
TR6 chr17 37880998 + G T TCGA-02-0252
Ins1 chr17 37880998 + G GT TCGA-02-0252
Del1 chr17 37880998 + GA G TCGA-02-0252
CSub1 chr2 39871235 + ATGCT GA TCGA-02-0252
Position is a 1-based open coordinate. For insertions and deletions, use the base before the insertion or the first base of the deletion as the reference base. If you do not have strand information from your sequencing results, it is likely that they are all reported on the + strand. Make sure that your reported reference base matches the base in the reported position in the hg19 reference sequence (or hg18 if you checked hg18 checkbox).
Amino-acid residue substitution format (separated by a tab or a space):
# UID / Transcript / AA change / Sample ID (optional)
TR1 NM_001126116.1 D127Y TCGA-02-0231
TR2 NM_001144919.1 R162Q TCGA-02-3512
TR3 NM_000321.2 Q702K TCGA-02-3532
TR4 NM_000245.2 A1108S TCGA-02-1523
TR5 NM_004333.4 V600E TCGA-02-0023
TR6 NM_001005862.1 G746V TCGA-02-0252
trascript identifier can be from either NCBI Refseq, CCDS, or Ensembl. Refseq and CCDS accessions can be specified without version numbers. The format of "AA change" column is (reference AA)(AA position)(alternate AA), without "(" and ")". Reference and alternate AAs should be from the 20 essential amino acids and each of them should be one amino acid-long.
Analysis
Analysis Type:
-Cancer driver analysis: This analysis predicts whether the submitted variants are cancer drivers or not.
-Functional effect analysis: This analysis predicts whether the submitted variants will have any functional effect on their translated proteins or not.
-Gene annotation only: This analysis provides GeneCard and PubMed information on the genes containing the submitted variants.
Currently, the following tissue types can be chosen at CRAVAT.
Name Full name Source Date
Bladder Bladder Urothelial Carcinoma BLCA (TCGA) Jun 2013
Blood-Lymphocyte Chronic Lymphocytic Leukemia CLL (ICGC) Mar 2013
Blood-Myeloid Acute Myeloid Leukemia LAML (TCGA) Jun 2013
Brain-Cerebellum Medulloblastoma MB (mixed source) Dec 2010
Brain-Glioblastoma-Multiforme Glioblastoma Multiforme GBM (TCGA) Jun 2013
Brain-Lower-Grade-Glioma Brain Lower Grade Glioma LGG (TCGA) Jun 2013
Breast Breast Invasive Carcinoma BRCA (TCGA) Jun 12012
Cervix Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma CESC (TCGA) Jun 2013
Colon Colon Adenocarcinoma COAD (TCGA) Jun 2013
Head and Neck Head and Neck Squamous Cell Carcinoma HNSC (TCGA) Jun 2013
Kidney-Chromophobe Kidney Chromophobe KICH (TCGA) Jun 2013
Kidney-Clear-Cell Kidney Renal Clear Cell Carcinoma KIRC (TCGA) Jun 2013
Kidney-Papillary-Cell Kidney Renal Papillary Cell Carcinoma KIRP (TCGA) Jun 2013
Liver-Nonviral Hepatocellular Carcinoma (Secondary to Alcohol and Adiposity) HCCA (ICGC) Mar 2013
Liver-Viral Hepatocellular Carcinoma (Viral) HCCV (ICGC) Mar 2013
Lung-Adenocarcinoma Lung Adenocarcinoma LUAD (TCGA) Jun 2013
Lung-Squamous Cell Lung Squamous Cell Carcinoma LUSC (TCGA) Jun 2013
Melanoma Melanoma ML (Yardena Samuels lab) Dec 2011
Other General purpose OV (TCGA) Jun 2013
Ovary Ovarian Serous Cystadenocarcinoma OV (TCGA) Jun 2013
Pancreas Pancreatic Cancer PNCC (ICGC)) Mar 2013
Prostate-Adenocarcinoma Prostate Adenocarcinoma PRAD (TCGA) Jun 2013
Rectum Rectum Adenocarcinoma READ (TCGA) Jun 2013
Skin Skin Cutaneous Melanoma SKCM (TCGA) Jun 2013
Stomach Stomach Adenocarcinoma STAD (TCGA) Jun 2013
Thyroid Thyroid Carcinoma THCA (TCGA) Jun 2013
Uterus Uterine Corpus Endometriod Carcinoma UCEC (TCGA) Jun 2013
Citation
If you use this tool please cite:
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.