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

ABSTRACT:

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.

SUBMITTER: Wong WC

PROVIDER: S-EPMC3137226 | biostudies-literature | 2011 Aug

REPOSITORIES: biostudies-literature

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

Wong Wing Chung WC Kim Dewey D Carter Hannah H Diekhans Mark M Ryan Michael C MC Karchin Rachel R

Bioinformatics (Oxford, England) 20110617 15

<h4>Summary</h4>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.<h4>Av ...[more]

PMID: 21685053

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