genome-music-mutation-relation (1p)

This document describes genome music mutation-relation version 0.04 (2013-05-14 at 16:03:04)

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 \s-1BAM\s0 files [sample_name, normal_bam, tumor_bam] (See Description)

maf-file Text

List of mutations in \s-1MAF\s0 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 \s-1MAF\s0 are tested.

skip-non-coding Boolean

Skip non-coding mutations from the provided \s-1MAF\s0 file Default value 'true' if not specified

skip-silent Boolean

Skip silent mutations from the provided \s-1MAF\s0 file Default value 'true' if not specified

This module parses a list of mutations in \s-1MAF\s0 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 \s-1BAM\s0 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 \s-1MAF\s0 file (16th column, with the header Tumor_Sample_Barcode).

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