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

GENOME-MUSIC(1p) User Contributed Perl Documentation GENOME-MUSIC(1p)

genome music

NAME

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

VERSION

This document describes genome music version 0.04 (2016-01-01 at 17:57:59)

SYNOPSIS

genome 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)
2016-01-01 perl v5.22.1