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


This document describes genome music mutation-relation version 0.04 (2016-01-01 at


genome 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.

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