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genome music - Mutational Significance in Cancer (Cancer Mutation Analysis)
This document describes genome music version 0.04 (2016-01-01 at 23:10:18)
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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.
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.
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.
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.