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.\"
.IX Title "GENOME-MUSIC-BMR 1p"
.TH GENOME-MUSIC-BMR 1p "2018-07-05" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.nh
.SH "genome music bmr"
.IX Header "genome music bmr"
.SH "NAME"
genome music bmr \- Calculate gene coverages and background mutation rates.
.SH "VERSION"
.IX Header "VERSION"
This document describes genome music bmr version 0.04 (2018\-07\-05 at 09:17:13)
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
genome music bmr ...
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
These tools are part of the MuSiC suite.
.SH "SUB-COMMANDS"
.IX Header "SUB-COMMANDS"
.SS "\s-1GENERAL\s0"
.IX Subsection "GENERAL"
.IP "\fBcalc-bmr\fR" 4
.IX Item "calc-bmr"
.RS 4
.PD 0
.ie n .IP "Calculates mutation rates given per-gene coverage (from ""music bmr calc-covg""), and a mutation list" 2
.el .IP "Calculates mutation rates given per-gene coverage (from ``music bmr calc-covg''), and a mutation list" 2
.IX Item "Calculates mutation rates given per-gene coverage (from music bmr calc-covg), and a mutation list"
.RE
.RS 4
.RE
.PD
.PP

.IP "\fBcalc-covg\fR" 4
.IX Item "calc-covg"
.RS 4
.PD 0
.IP "Uses calcRoiCovg.c to count covered bases per-gene for each given tumor-normal pair of BAMs." 2
.IX Item "Uses calcRoiCovg.c to count covered bases per-gene for each given tumor-normal pair of BAMs."
.RE
.RS 4
.RE
.PD
.PP

.IP "\fBcalc-covg-helper\fR" 4
.IX Item "calc-covg-helper"
.RS 4
.PD 0
.IP "Uses calcRoiCovg.c to count covered bases per-gene for a tumor-normal pair of BAMs." 2
.IX Item "Uses calcRoiCovg.c to count covered bases per-gene for a tumor-normal pair of BAMs."
.RE
.RS 4
.RE
.PD
.PP

.IP "\fBcalc-wig-covg\fR" 4
.IX Item "calc-wig-covg"
.RS 4
.PD 0
.IP "Count covered bases per-gene for each given wiggle track format file." 2
.IX Item "Count covered bases per-gene for each given wiggle track format file."
.RE
.RS 4
.RE
.PD
.PP

.SH "LICENSE"
.IX Header "LICENSE"
Copyright (C) 2010\-2011 Washington University in St. Louis.
.PP
It is released under the Lesser \s-1GNU\s0 Public License (\s-1LGPL\s0) version 3.  See the 
associated \s-1LICENSE\s0 file in this distribution.
.SH "AUTHORS"
.IX Header "AUTHORS"
.Vb 1
\& Cyriac Kandoth, Ph.D.
.Ve
.SH "SEE ALSO"
.IX Header "SEE ALSO"
\&\fBgenome-music-bmr-calc-covg\fR(1),
\&\fBgenome-music-bmr-calc-bmr\fR(1),
\&\fBgenome-music\fR(1),
\&\fBgenome\fR(1)