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 0.04 (2016-01-01 at
       23:10:18)

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.