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Bioinformatics. 2011 Aug 1;27(15):2147-8. doi: 10.1093/bioinformatics/btr357. Epub 2011 Jun 17.

CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer.

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  • 1Department of Biomedical Engineering and Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, USA.



Thousands of cancer exomes are currently being sequenced, yielding millions of non-synonymous single nucleotide variants (SNVs) of possible relevance to disease etiology. Here, we provide a software toolkit to prioritize SNVs based on their predicted contribution to tumorigenesis. It includes a database of precomputed, predictive features covering all positions in the annotated human exome and can be used either stand-alone or as part of a larger variant discovery pipeline.


MySQL database, source code and binaries freely available for academic/government use at, Source in Python and C++. Requires 32 or 64-bit Linux system (tested on Fedora Core 8,10,11 and Ubuntu 10), 2.5*≤ Python <3.0*, MySQL server >5.0, 60 GB available hard disk space (50 MB for software and data files, 40 GB for MySQL database dump when uncompressed), 2 GB of RAM.

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