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.IX Title "GENOME-MUSIC-BMR-CALC-WIG-COVG 1p"
.TH GENOME-MUSIC-BMR-CALC-WIG-COVG 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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.SH "genome music bmr calc-wig-covg"
.IX Header "genome music bmr calc-wig-covg"
.SH "NAME"
genome music bmr calc\-wig\-covg \- Count covered bases per\-gene for each given wiggle track format file.
.SH "VERSION"
.IX Header "VERSION"
This document describes genome music bmr calc-wig-covg version 0.04 (2018\-07\-05 at 09:17:13)
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
genome music bmr calc-wig-covg \-\-roi\-file=? \-\-reference\-sequence=? \-\-wig\-list=? \-\-output\-dir=?
.PP
General usage:
.PP
.Vb 5
\& ... music bmr calc\-wig\-covg \e
\&    \-\-wig\-list input_dir/wig_list \e
\&    \-\-output\-dir output_dir/ \e
\&    \-\-reference\-sequence input_dir/all_sequences.fa \e
\&    \-\-roi\-file input_dir/all_coding_exons.tsv
.Ve
.SH "REQUIRED ARGUMENTS"
.IX Header "REQUIRED ARGUMENTS"
.IP "roi-file  \fIText\fR" 4
.IX Item "roi-file Text"
Tab-delimited list of ROIs [chr start stop gene_name] (See Description)
.IP "reference-sequence  \fIText\fR" 4
.IX Item "reference-sequence Text"
Path to reference sequence in \s-1FASTA\s0 format
.IP "wig-list  \fIText\fR" 4
.IX Item "wig-list Text"
Tab-delimited list of \s-1WIG\s0 files [sample_name wig_file] (See Description)
.IP "output-dir  \fIText\fR" 4
.IX Item "output-dir Text"
Directory where output files and subdirectories will be written
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This script counts bases with sufficient coverage in the ROIs of each gene from given wiggle track
format files, and categorizes them into \- \s-1AT, CG\s0 (non-CpG), and CpG counts. It also adds
up these base-counts across all ROIs of each gene for each sample, but covered bases that lie
within overlapping ROIs are not counted more than once towards these total counts.
.SH "ARGUMENTS"
.IX Header "ARGUMENTS"
.IP "\-\-roi\-file" 4
.IX Item "--roi-file"
.RS 4
.PD 0
.IP "The regions of interest (ROIs) of each gene are typically regions targeted for sequencing or are merged exon loci (from multiple transcripts) of genes with 2\-bp flanks (splice junctions). For per-gene base counts, an overlapping base will be counted each time it appears in an \s-1ROI\s0 of the same gene. To avoid this, be sure to merge together overlapping ROIs of the same gene. BEDtools' mergeBed can help if used per gene." 8
.IX Item "The regions of interest (ROIs) of each gene are typically regions targeted for sequencing or are merged exon loci (from multiple transcripts) of genes with 2-bp flanks (splice junctions). For per-gene base counts, an overlapping base will be counted each time it appears in an ROI of the same gene. To avoid this, be sure to merge together overlapping ROIs of the same gene. BEDtools' mergeBed can help if used per gene."
.RE
.RS 4
.RE
.IP "\-\-reference\-sequence" 4
.IX Item "--reference-sequence"
.RS 4
.IP "The reference sequence in \s-1FASTA\s0 format. If a reference sequence index is not found next to this file (a .fai file), it will be created." 8
.IX Item "The reference sequence in FASTA format. If a reference sequence index is not found next to this file (a .fai file), it will be created."
.RE
.RS 4
.RE
.IP "\-\-wig\-list" 4
.IX Item "--wig-list"
.RS 4
.IP "Provide a file containing sample names and the wiggle track format file locations for each. Use the tab-delimited format [sample_name wig_file] per line. Additional columns like clinical data are allowed, but ignored. 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 the wiggle track format file locations for each. Use the tab-delimited format [sample_name wig_file] per line. Additional columns like clinical data are allowed, but ignored. 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
.IP "\-\-output\-dir" 4
.IX Item "--output-dir"
.RS 4
.IP "Specify an output directory where the following will be created/written: roi_covgs: Subdirectory containing per-ROI covered base counts for each sample. gene_covgs: Subdirectory containing per-gene covered base counts for each sample. total_covgs: File containing the overall non-overlapping coverages per sample." 8
.IX Item "Specify an output directory where the following will be created/written: roi_covgs: Subdirectory containing per-ROI covered base counts for each sample. gene_covgs: Subdirectory containing per-gene covered base counts for each sample. total_covgs: File containing the overall non-overlapping coverages per sample."
.RE
.RS 4
.RE
.PD
.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\fR(1),
\&\fBgenome-music\fR(1),
\&\fBgenome\fR(1)