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.\" ========================================================================
.\"
.IX Title "GENOME-MUSIC-MUTATION-RELATION 1p"
.TH GENOME-MUSIC-MUTATION-RELATION 1p "2018-07-05" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.nh
.SH "genome music mutation-relation"
.IX Header "genome music mutation-relation"
.SH "NAME"
genome music mutation\-relation \- Identify relationships of mutation concurrency or mutual exclusivity in genes across cases.
.SH "VERSION"
.IX Header "VERSION"
This document describes genome music mutation-relation version 0.04 (2018\-07\-05 at 09:17:13)
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
genome music mutation-relation \-\-bam\-list=? \-\-maf\-file=? \-\-output\-file=? [\-\-mutation\-matrix\-file=?] [\-\-permutations=?] [\-\-gene\-list=?] [\-\-skip\-non\-coding] [\-\-skip\-silent]
.PP
.Vb 4
\& ... music mutation\-relation \e
\&        \-\-maf\-file /path/myMAF.tsv \e
\&        \-\-permutations 1000 \e
\&        \-\-output\-file /path/mutation_relation.csv
.Ve
.SH "REQUIRED ARGUMENTS"
.IX Header "REQUIRED ARGUMENTS"
.IP "bam-list  \fIText\fR" 4
.IX Item "bam-list Text"
Tab delimited list of \s-1BAM\s0 files [sample_name, normal_bam, tumor_bam] (See Description)
.IP "maf-file  \fIText\fR" 4
.IX Item "maf-file Text"
List of mutations in \s-1MAF\s0 format
.IP "output-file  \fIText\fR" 4
.IX Item "output-file Text"
Results of mutation-relation tool
.SH "OPTIONAL ARGUMENTS"
.IX Header "OPTIONAL ARGUMENTS"
.IP "mutation-matrix-file  \fIText\fR" 4
.IX Item "mutation-matrix-file Text"
Optionally store the sample-vs-gene matrix used during calculations.
.IP "permutations  \fINumber\fR" 4
.IX Item "permutations Number"
Number of permutations used to determine P\-values
.Sp
Default value '100' if not specified
.IP "gene-list  \fIText\fR" 4
.IX Item "gene-list Text"
List of genes to test, typically SMGs. If unspecified, all genes in \s-1MAF\s0 are tested.
.IP "skip-non-coding  \fIBoolean\fR" 4
.IX Item "skip-non-coding Boolean"
Skip non-coding mutations from the provided \s-1MAF\s0 file
.Sp
Default value 'true' if not specified
.IP "noskip-non-coding  \fIBoolean\fR" 4
.IX Item "noskip-non-coding Boolean"
Make skip-non-coding 'false'
.IP "skip-silent  \fIBoolean\fR" 4
.IX Item "skip-silent Boolean"
Skip silent mutations from the provided \s-1MAF\s0 file
.Sp
Default value 'true' if not specified
.IP "noskip-silent  \fIBoolean\fR" 4
.IX Item "noskip-silent Boolean"
Make skip-silent 'false'
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
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.
.SH "ARGUMENTS"
.IX Header "ARGUMENTS"
.IP "\-\-bam\-list" 4
.IX Item "--bam-list"
.RS 4
.PD 0
.IP "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)." 8
.IX Item "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)."
.RE
.RS 4
.RE
.PD
.SH "AUTHORS"
.IX Header "AUTHORS"
.Vb 2
\& Nathan D. Dees, Ph.D.
\& Qunyuan Zhang, Ph.D.
.Ve