gmt-music1p

Usage

gmt music

Version

This document describes gmt music version 0.04 (2020-11-06 at 21:54:23)

Overview

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:

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Do not use headers

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4 columns, which are [chromosome start-position(1-based) stop-position(1-based) gene_name]

4. Clinical Data Files:

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Headers are required

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At least 1 sample_id column and 1 attribute column, with the format being [sample_id clinical_data_attribute clinical_data_attribute ...]

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The sample_id must match the sample_id listed in the MAF under "Tumor_Sample_Barcode" for relating the mutations of this sample.

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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.

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/