OnWorks favicon

gmt-music-mutation-relationp - Online in the Cloud

Run gmt-music-mutation-relationp in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command gmt-music-mutation-relationp 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



gmt music mutation-relation - Identify relationships of mutation concurrency or mutual
exclusivity in genes across cases.


This document describes gmt music mutation-relation version 0.04 (2016-01-01 at 23:10:19)


gmt music mutation-relation --bam-list=? --maf-file=? --output-file=?
[--mutation-matrix-file=?] [--permutations=?] [--gene-list=?] [--skip-non-coding]

... music mutation-relation \
--maf-file /path/myMAF.tsv \
--permutations 1000 \
--output-file /path/mutation_relation.csv


bam-list Text
Tab delimited list of BAM files [sample_name, normal_bam, tumor_bam] (See Description)

maf-file Text
List of mutations in MAF format

output-file Text
Results of mutation-relation tool


mutation-matrix-file Text
Optionally store the sample-vs-gene matrix used during calculations.

permutations Number
Number of permutations used to determine P-values

Default value '100' if not specified

gene-list Text
List of genes to test, typically SMGs. If unspecified, all genes in MAF are tested.

skip-non-coding Boolean
Skip non-coding mutations from the provided MAF file

Default value 'true' if not specified

noskip-non-coding Boolean
Make skip-non-coding 'false'

skip-silent Boolean
Skip silent mutations from the provided MAF file

Default value 'true' if not specified

noskip-silent Boolean
Make skip-silent 'false'


This module parses a list of mutations in MAF format and attempts to determine
relationships among mutated genes. It employs a correlation test to see whether or not any
two genes are mutated concurrently (positive correlation) or mutually exclusively
(negative correlation). Because of the possibility of largely varying numbers of mutations
present in different genes, P-values are calculated using restricted permutations that
take into account the distribution of mutation counts among the samples. In the output
file, 'pand' is the P-value for concurrent mutation events, and 'pexc' is the P-value for
mutually exclusive mutation events.


Provide a file containing sample names and normal/tumor BAM locations for each. Use
the tab- delimited format [sample_name normal_bam tumor_bam] per line. This tool only
needs sample_name, so all other columns can be skipped. The sample_name must be the
same as the tumor sample names used in the MAF file (16th column, with the header


Nathan D. Dees, Ph.D.
Qunyuan Zhang, Ph.D.

Use gmt-music-mutation-relationp online using onworks.net services

Free Servers & Workstations

Download Windows & Linux apps

  • 1
    Phaser is a fast, free, and fun open
    source HTML5 game framework that offers
    WebGL and Canvas rendering across
    desktop and mobile web browsers. Games
    can be co...
    Download Phaser
  • 2
    VASSAL Engine
    VASSAL Engine
    VASSAL is a game engine for creating
    electronic versions of traditional board
    and card games. It provides support for
    game piece rendering and interaction,
    Download VASSAL Engine
  • 3
    OpenPDF - Fork of iText
    OpenPDF - Fork of iText
    OpenPDF is a Java library for creating
    and editing PDF files with a LGPL and
    MPL open source license. OpenPDF is the
    LGPL/MPL open source successor of iText,
    Download OpenPDF - Fork of iText
  • 4
    SAGA - System for Automated
    Geoscientific Analyses - is a Geographic
    Information System (GIS) software with
    immense capabilities for geodata
    processing and ana...
    Download SAGA GIS
  • 5
    Toolbox for Java/JTOpen
    Toolbox for Java/JTOpen
    The IBM Toolbox for Java / JTOpen is a
    library of Java classes supporting the
    client/server and internet programming
    models to a system running OS/400,
    i5/OS, o...
    Download Toolbox for Java/JTOpen
  • 6
    D3.js (or D3 for Data-Driven Documents)
    is a JavaScript library that allows you
    to produce dynamic, interactive data
    visualizations in web browsers. With D3
    Download D3.js
  • More »

Linux commands