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.IX Title "GENOME-MUSIC 1p"
.TH GENOME-MUSIC 1p "2020-11-06" "perl v5.30.3" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "genome music"
.IX Header "genome music"
.SH "NAME"
genome music \- Mutational Significance in Cancer (Cancer Mutation Analysis)
.SH "VERSION"
.IX Header "VERSION"
This document describes genome music version 0.04 (2020\-11\-06 at 21:54:23)
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
genome 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 "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)