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PROGRAM:

NAME

gmt music - Mutational Significance in Cancer (Cancer Mutation Analysis)

VERSION

This document describes gmt music version 0.04 (2016-01-01 at 23:10:18)

SYNOPSIS

gmt music ...

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:

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.

SUB-COMMANDS

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.

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