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.\"
.IX Title "GMT-MUSIC-BMR-CALC-COVG-HELPER 1p"
.TH GMT-MUSIC-BMR-CALC-COVG-HELPER 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 "gmt music bmr calc-covg-helper"
.IX Header "gmt music bmr calc-covg-helper"
.SH "NAME"
gmt music bmr calc\-covg\-helper \- Uses calcRoiCovg.c to count covered bases per\-gene for a tumor\-normal pair of BAMs.
.SH "VERSION"
.IX Header "VERSION"
This document describes gmt music bmr calc-covg-helper version 0.04 (2018\-07\-05 at 09:17:13)
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
gmt music bmr calc-covg-helper \-\-roi\-file=? \-\-reference\-sequence=? \-\-normal\-tumor\-bam\-pair=? [\-\-output\-file=?] [\-\-output\-dir=?] [\-\-normal\-min\-depth=?] [\-\-tumor\-min\-depth=?] [\-\-min\-mapq=?]
.PP
General usage:
.PP
.Vb 5
\& ... music bmr calc\-covg\-helper \e
\&    \-\-normal\-tumor\-bam\-pair "sample\-name path/to/normal_bam path/to/tumor_bam" \e
\&    \-\-reference\-sequence input_dir/all_sequences.fa \e
\&    \-\-output\-file output_file \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 "normal-tumor-bam-pair  \fIText\fR" 4
.IX Item "normal-tumor-bam-pair Text"
Tab delimited line with sample name, path to normal bam file, and path to tumor bam file (See Description)
.SH "OPTIONAL ARGUMENTS"
.IX Header "OPTIONAL ARGUMENTS"
.IP "output-file  \fIText\fR" 4
.IX Item "output-file Text"
Output file path.  Specify either output-file or output-directory.
.IP "output-dir  \fIText\fR" 4
.IX Item "output-dir Text"
Output directory path.  Specify either output-file or output-directory
.IP "normal-min-depth  \fIInteger\fR" 4
.IX Item "normal-min-depth Integer"
The minimum read depth to consider a Normal \s-1BAM\s0 base as covered
.Sp
Default value '6' if not specified
.IP "tumor-min-depth  \fIInteger\fR" 4
.IX Item "tumor-min-depth Integer"
The minimum read depth to consider a Tumor \s-1BAM\s0 base as covered
.Sp
Default value '8' if not specified
.IP "min-mapq  \fIInteger\fR" 4
.IX Item "min-mapq Integer"
The minimum mapping quality of reads to consider towards read depth counts
.Sp
Default value '20' if not specified
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This script counts bases with sufficient coverage in the ROIs of each gene in the given pair of
tumor-normal \s-1BAM\s0 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 in the 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). ROIs from the same chromosome must be listed adjacent to each other in this file. This allows the underlying C\-based code to run much more efficiently and avoid re-counting bases seen in overlapping ROIs (for overall covered base counts). 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). ROIs from the same chromosome must be listed adjacent to each other in this file. This allows the underlying C-based code to run much more efficiently and avoid re-counting bases seen in overlapping ROIs (for overall covered base counts). 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 "\-\-normal\-tumor\-bam\-pair" 4
.IX Item "--normal-tumor-bam-pair"
.RS 4
.ie n .IP """sample-name path/to/normal_bam path/to/tumor_bam""" 8
.el .IP "``sample-name path/to/normal_bam path/to/tumor_bam''" 8
.IX Item "sample-name path/to/normal_bam path/to/tumor_bam"
.RE
.RS 4
.RE
.IP "\-\-output\-file" 4
.IX Item "--output-file"
.RS 4
.IP "Specify an output file where the per-ROI covered base counts will be written" 8
.IX Item "Specify an output file where the per-ROI covered base counts will be written"
.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)