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genome :: music :: mutation-relation

genome music mutation-relation

NAME

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


VERSION

This document describes genome music mutation-relation version 0.0401 (2014-02-13 at 08:01:08)


SYNOPSIS

genome 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

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


OPTIONAL ARGUMENTS

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'


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

--bam-list
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 Tumor_Sample_Barcode).

AUTHORS

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


Versions