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.\" ========================================================================
.\"
.IX Title "GENOME-MUSIC-PROXIMITY 1p"
.TH GENOME-MUSIC-PROXIMITY 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 proximity"
.IX Header "genome music proximity"
.SH "NAME"
genome music proximity \- Perform a proximity analysis on a list of mutations.
.SH "VERSION"
.IX Header "VERSION"
This document describes genome music proximity version 0.04 (2018\-07\-05 at 09:17:13)
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
genome music proximity \-\-maf\-file=? \-\-output\-file=? \-\-output\-dir=? [\-\-max\-proximity=?] [\-\-skip\-non\-coding] [\-\-skip\-silent]
.PP
.Vb 4
\& ... music proximity \e
\&        \-\-maf\-file input_dir/myMAF.tsv \e
\&        \-\-output\-dir output_dir/ \e
\&        \-\-max\-proximity 15
.Ve
.SH "REQUIRED ARGUMENTS"
.IX Header "REQUIRED ARGUMENTS"
.IP "maf-file  \fIText\fR" 4
.IX Item "maf-file Text"
List of mutations using \s-1TCGA MAF\s0 specifications v2.3
.IP "output-file  \fIText\fR" 4
.IX Item "output-file Text"
\&\s-1TODO\s0
.IP "output-dir  \fIText\fR" 4
.IX Item "output-dir Text"
Directory where output files will be written
.SH "OPTIONAL ARGUMENTS"
.IX Header "OPTIONAL ARGUMENTS"
.IP "max-proximity  \fIText\fR" 4
.IX Item "max-proximity Text"
Maximum allowed \s-1AA\s0 distance between 2 mutations
.Sp
Default value '7' if not specified
.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 first calculates the amino acid position of each mutation in the \s-1MAF\s0 file within its
respective transcript. Then, for each mutation, two values are calculated: 1) the number of other
mutations on the same transcript within the proximity limit set by the max-proximity input
parameter, and 2) the distance to the closest other mutation in this nearby set. Only mutations
which have another mutation within close proximity are reported in the output-file.
.PP
In addition to the standard version 2.3 \s-1MAF\s0 headers, there needs to be 3 columns appended. These
column headers in the \s-1MAF\s0 must have these names in the header in order for the tool to find them:
   transcript_name \- the transcript name, such as \s-1NM_000028\s0
 amino_acid_change \- the amino acid change, such as p.R290H
        c_position \- the nucleotide position changed, such as c.869
.PP
The output is generated with the following column headers:
Mutations_Within_Proximity, Nearest_Mutation, Gene, Transcript, Affected_Amino_Acid(s), Chr,
Start, Stop, Ref_Allele, Var_Allele, Sample
.SH "AUTHORS"
.IX Header "AUTHORS"
.Vb 3
\& Nathan D. Dees, Ph.D.
\& Dan Koboldt, M.S.
\& Cyriac Kandoth, Ph.D.
.Ve