This is the command gmt-musicp that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
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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