gmt music

NAME

       gmt music - Mutational Significance in Cancer (Cancer Mutation Analysis)

VERSION

       This document describes gmt music version 0.04 (2013-05-25 at 17:45:01)

SYNOPSIS

       gmt music ...

DESCRIPTION

       The MuSiC suite is a set of tools aimed at discovering the significance of somatic
       mutations found within a given cohort of cancer samples, and with respect to a variety of
       external data sources. The standard inputs required are:

       1. mapped reads in BAM format
       2. predicted or validated SNVs or indels in mutation annotation format (MAF)
       3. a list of regions of interest (typically the boundaries of coding exons)
       4. any relevant numeric or categorical clinical data.

       The formats for inputs 3. and 4. are:

       3. Regions of Interest File:
           ·   Do not use headers

           ·   4 columns, which are [chromosome  start-position(1-based)  stop-position(1-based)
               gene_name]

       4. Clinical Data Files:
           ·   Headers are required

           ·   At least 1 sample_id column and 1 attribute column, with the format being
               [sample_id  clinical_data_attribute  clinical_data_attribute  ...]

           ·   The sample_id must match the sample_id listed in the MAF under
               "Tumor_Sample_Barcode" for relating the mutations of this sample.

           ·   The header for each clinical_data_attribute will appear in the output file to
               denote relationships with the mutation data from the MAF.

       Descriptions for the usage of each tool (each sub-command) can be found separately.

       The play command runs all of the sub-commands serially on a selected input set.

SUB-COMMANDS

   GENERAL
       bmr
           Calculate gene coverages and background mutation rates.

       clinical-correlation
           Correlate phenotypic traits against mutated genes, or against individual variants

       cosmic-omim
           Compare the amino acid changes of supplied mutations to COSMIC and OMIM databases.

       galaxy
           Run the full suite of MuSiC tools sequentially.

       mutation-relation
           Identify relationships of mutation concurrency or mutual exclusivity in genes across
           cases.

       path-scan
           Find signifcantly mutated pathways in a cohort given a list of somatic mutations.

       pfam
           Add Pfam annotation to a MAF file

       play
           Run the full suite of MuSiC tools sequentially.

       plot
           Generate relevant plots and visualizations for MuSiC.

       proximity
           Perform a proximity analysis on a list of mutations.

       smg
           Identify significantly mutated genes.

       survival
           Create survival plots and P-values for clinical and mutational phenotypes.

LICENSE

       Copyright (C) 2007-2011 Washington University in St. Louis.

       It is released under the Lesser GNU Public License (LGPL) version 3.  See the associated
       LICENSE file in this distribution.

AUTHORS

       This software is developed by the analysis and engineering teams at The Genome Institute
       at Washington University School of Medicine in St. Louis, with funding from the National
       Human Genome Research Institute.  Richard K. Wilson, P.I.

       The primary authors of the MuSiC suite are:

        Nathan D. Dees, Ph.D.
        Cyriac Kandoth, Ph.D.
        Dan Koboldt, M.S.
        William Schierding, M.S.
        Michael Wendl, Ph.D.
        Qunyuan Zhang, Ph.D.
        Thomas B. Mooney, M.S.

CREDITS

       The MuSiC suite uses tabix, by Heng Li.  See http://samtools.sourceforge.net/tabix.shtml.

       MuSiC depends on copies of data from the following databases, packaged in a form useable
       for quick analysis:

        * KEGG - http://www.genome.jp/kegg/
        * COSMIC - http://www.sanger.ac.uk/genetics/CGP/cosmic/
        * OMIM - http://www.ncbi.nlm.nih.gov/omim
        * Pfam - http://pfam.sanger.ac.uk/
        * SMART - http://smart.embl-heidelberg.de/
        * SUPERFAMILY - http://supfam.cs.bris.ac.uk/SUPERFAMILY/
        * PatternScan - http://www.expasy.ch/prosite/

BUGS

       For defects with any software in the genome namespace, contact
        genome-dev ~at~ genome.wustl.edu.

SEE ALSO

       genome(1)