General Information
| Description | Toolkit for detecting biologically important single nucleotide mutations in cancer |
| Homepage | http://wiki.chasmsoftware.org |
Publications
CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer
Summary:
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.
Availability and Implementation:
MySQL database, source code and binaries freely available for academic/government use at http://wiki.chasmsoftware.org, 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.
Contact:
karchin@jhu.edu
Supplementary Information:
Supplementary data are available at Bioinformatics online.
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