Introduction

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 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.

Publications

  1. CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer.
    Cite this
    Wong WC, Kim D, Carter H, Diekhans M, Ryan MC, Karchin R, 2011-08-01 - Bioinformatics (Oxford, England)
  2. Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations.
    Cite this
    Carter H, Chen S, Isik L, Tyekucheva S, Velculescu VE, Kinzler KW, Vogelstein B, Karchin R, 2009-08-01 - Cancer research

Credits

  1. Wing Chung Wong
    Developer

    Department of Biomedical Engineering and Institute for Computational Medicine, Johns Hopkins University, United States of America

  2. Dewey Kim
    Developer

  3. Hannah Carter
    Developer

  4. Mark Diekhans
    Developer

  5. Michael C Ryan
    Developer

  6. Rachel Karchin
    Investigator

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Summary
AccessionBT003396
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Submitted ByRachel Karchin