CHASM Scores

Created By Melissa Cline MelissaCline
CHASM is a method to predict the functional significance of somatic missense variants. See PMID: 21685053. CRAVAT (http://www.cravat.us/) is a web-based version of CHASM with pre-computed predictors for selected cancer types. When CRAVAT contained a predictor appropriate to the MAF, CRAVAT was used with the predictor to generate the output. In other cases, a new predictor was trained by the Rachel Karchin lab at JHU. For each missense mutation, these output files identify the mutation by genomic coordinates and amino acid change, and report a score, p-value, and FDR-corrected q-value describing the functional significance of the change. For more information, see the indicated publications, or contact Rachel Karchin at karchin at jhu.edu. Special thanks to Rachel Karchin and Noushin Niknafs.

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