Provided by: libgenome-model-tools-music-perl_0.04-4_all
genome music mutation-relation
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 (2018-07-05 at 09:17:13)
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
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.
--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).
Nathan D. Dees, Ph.D. Qunyuan Zhang, Ph.D.