gmt-music (1p)

This document describes gmt music version 0.04 (2013-05-14 at 16:03:04)

gmt music ...

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 \s-1BAM\s0 format

2. predicted or validated SNVs or indels in mutation annotation format (\s-1MAF\s0)

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 \s-1MAF\s0 under \*(L"Tumor_Sample_Barcode\*(R" 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 \s-1MAF\s0.

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.

\s-1GENERAL\s0

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 \s-1COSMIC\s0 and \s-1OMIM\s0 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 \s-1MAF\s0 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.

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

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.

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.

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/

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

genome(1)