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.\" ========================================================================
.\"
.IX Title "GMT-MUSIC 1p"
.TH GMT-MUSIC 1p "2016-01-01" "perl v5.22.1" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "gmt music"
.IX Header "gmt music"
.SH "NAME"
gmt music \- Mutational Significance in Cancer (Cancer Mutation Analysis)
.SH "VERSION"
.IX Header "VERSION"
This document describes gmt music version 0.04 (2016\-01\-01 at 17:58:00)
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
gmt music ...
.SH "DESCRIPTION"
.IX Header "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:
.IP "1. mapped reads in \s-1BAM\s0 format" 4
.IX Item "1. mapped reads in BAM format"
.PD 0
.IP "2. predicted or validated SNVs or indels in mutation annotation format (\s-1MAF\s0)" 4
.IX Item "2. predicted or validated SNVs or indels in mutation annotation format (MAF)"
.IP "3. a list of regions of interest (typically the boundaries of coding exons)" 4
.IX Item "3. a list of regions of interest (typically the boundaries of coding exons)"
.IP "4. any relevant numeric or categorical clinical data." 4
.IX Item "4. any relevant numeric or categorical clinical data."
.PD
.PP
The formats for inputs 3. and 4. are:
.IP "3. Regions of Interest File:" 4
.IX Item "3. Regions of Interest File:"
.RS 4
.PD 0
.IP "\(bu" 4
.PD
Do not use headers
.IP "\(bu" 4
4 columns, which are [chromosome  start\-position(1\-based)  stop\-position(1\-based)  gene_name]
.RE
.RS 4
.RE
.IP "4. Clinical Data Files:" 4
.IX Item "4. Clinical Data Files:"
.RS 4
.PD 0
.IP "\(bu" 4
.PD
Headers are required
.IP "\(bu" 4
At least 1 sample_id column and 1 attribute column, with the format being [sample_id  clinical_data_attribute  clinical_data_attribute  ...]
.IP "\(bu" 4
The sample_id must match the sample_id listed in the \s-1MAF\s0 under \*(L"Tumor_Sample_Barcode\*(R" for relating the mutations of this sample.
.IP "\(bu" 4
The header for each clinical_data_attribute will appear in the output file to denote relationships with the mutation data from the \s-1MAF.\s0
.RE
.RS 4
.RE
.PP
Descriptions for the usage of each tool (each sub-command) can be found separately.
.PP
The \fBplay\fR command runs all of the sub-commands serially on a selected input set.
.SH "SUB-COMMANDS"
.IX Header "SUB-COMMANDS"
.SS "\s-1GENERAL\s0"
.IX Subsection "GENERAL"
.IP "\fBbmr\fR" 4
.IX Item "bmr"
.RS 4
.PD 0
.IP "Calculate gene coverages and background mutation rates." 2
.IX Item "Calculate gene coverages and background mutation rates."
.RE
.RS 4
.RE
.PD
.PP

.IP "\fBclinical-correlation\fR" 4
.IX Item "clinical-correlation"
.RS 4
.PD 0
.IP "Correlate phenotypic traits against mutated genes, or against individual variants" 2
.IX Item "Correlate phenotypic traits against mutated genes, or against individual variants"
.RE
.RS 4
.RE
.PD
.PP

.IP "\fBcosmic-omim\fR" 4
.IX Item "cosmic-omim"
.RS 4
.PD 0
.IP "Compare the amino acid changes of supplied mutations to \s-1COSMIC\s0 and \s-1OMIM\s0 databases." 2
.IX Item "Compare the amino acid changes of supplied mutations to COSMIC and OMIM databases."
.RE
.RS 4
.RE
.PD
.PP

.IP "\fBgalaxy\fR" 4
.IX Item "galaxy"
.RS 4
.PD 0
.IP "Run the full suite of MuSiC tools sequentially." 2
.IX Item "Run the full suite of MuSiC tools sequentially."
.RE
.RS 4
.RE
.PD
.PP

.IP "\fBmutation-relation\fR" 4
.IX Item "mutation-relation"
.RS 4
.PD 0
.IP "Identify relationships of mutation concurrency or mutual exclusivity in genes across cases." 2
.IX Item "Identify relationships of mutation concurrency or mutual exclusivity in genes across cases."
.RE
.RS 4
.RE
.PD
.PP

.IP "\fBpath-scan\fR" 4
.IX Item "path-scan"
.RS 4
.PD 0
.IP "Find signifcantly mutated pathways in a cohort given a list of somatic mutations." 2
.IX Item "Find signifcantly mutated pathways in a cohort given a list of somatic mutations."
.RE
.RS 4
.RE
.PD
.PP

.IP "\fBpfam\fR" 4
.IX Item "pfam"
.RS 4
.PD 0
.IP "Add Pfam annotation to a \s-1MAF\s0 file" 2
.IX Item "Add Pfam annotation to a MAF file"
.RE
.RS 4
.RE
.PD
.PP

.IP "\fBplay\fR" 4
.IX Item "play"
.RS 4
.PD 0
.IP "Run the full suite of MuSiC tools sequentially." 2
.IX Item "Run the full suite of MuSiC tools sequentially."
.RE
.RS 4
.RE
.PD
.PP

.IP "\fBplot\fR" 4
.IX Item "plot"
.RS 4
.PD 0
.IP "Generate relevant plots and visualizations for MuSiC." 2
.IX Item "Generate relevant plots and visualizations for MuSiC."
.RE
.RS 4
.RE
.PD
.PP

.IP "\fBproximity\fR" 4
.IX Item "proximity"
.RS 4
.PD 0
.IP "Perform a proximity analysis on a list of mutations." 2
.IX Item "Perform a proximity analysis on a list of mutations."
.RE
.RS 4
.RE
.PD
.PP

.IP "\fBsmg\fR" 4
.IX Item "smg"
.RS 4
.PD 0
.IP "Identify significantly mutated genes." 2
.IX Item "Identify significantly mutated genes."
.RE
.RS 4
.RE
.PD
.PP

.IP "\fBsurvival\fR" 4
.IX Item "survival"
.RS 4
.PD 0
.IP "Create survival plots and P\-values for clinical and mutational phenotypes." 2
.IX Item "Create survival plots and P-values for clinical and mutational phenotypes."
.RE
.RS 4
.RE
.PD
.PP

.SH "LICENSE"
.IX Header "LICENSE"
Copyright (C) 2007\-2011 Washington University in St. Louis.
.PP
It is released under the Lesser \s-1GNU\s0 Public License (\s-1LGPL\s0) version 3.  See the 
associated \s-1LICENSE\s0 file in this distribution.
.SH "AUTHORS"
.IX Header "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.
.PP
The primary authors of the MuSiC suite are:
.PP
.Vb 7
\& 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.
.Ve
.SH "CREDITS"
.IX Header "CREDITS"
The MuSiC suite uses tabix, by Heng Li.  See http://samtools.sourceforge.net/tabix.shtml.
.PP
MuSiC depends on copies of data from the following databases, packaged in a form useable for quick analysis:
.PP
.Vb 7
\& * 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/
.Ve
.SH "BUGS"
.IX Header "BUGS"
For defects with any software in the genome namespace, contact
 genome-dev ~at~ genome.wustl.edu.
.SH "SEE ALSO"
.IX Header "SEE ALSO"
\&\fBgenome\fR(1)