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GMT-MUSIC-MUTATION-RELATION(1p) User Contributed Perl Documentation GMT-MUSIC-MUTATION-RELATION(1p)

gmt music mutation-relation

NAME

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

VERSION

This document describes gmt music mutation-relation version 0.04 (2018-07-05 at 09:17:13)

SYNOPSIS

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

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

REQUIRED ARGUMENTS

Tab delimited list of BAM files [sample_name, normal_bam, tumor_bam] (See Description)
List of mutations in MAF format
Results of mutation-relation tool

OPTIONAL ARGUMENTS

Optionally store the sample-vs-gene matrix used during calculations.
Number of permutations used to determine P-values

Default value '100' if not specified

List of genes to test, typically SMGs. If unspecified, all genes in MAF are tested.
Skip non-coding mutations from the provided MAF file

Default value 'true' if not specified

Make skip-non-coding 'false'
Skip silent mutations from the provided MAF file

Default value 'true' if not specified

Make skip-silent 'false'

DESCRIPTION

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.

ARGUMENTS

AUTHORS

 Nathan D. Dees, Ph.D.
 Qunyuan Zhang, Ph.D.
2018-07-05 perl v5.26.2