GMT-MUSIC(1p)

gmt music

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

VERSION
This document describes gmt music version 0.04 (2018-07-05 at 09:17:13)

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 significantly 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)