bamdamage - Generates damage plots for a bam file.
bamdamage [--mapquality qual] [--basequality qual] [--sample name] [file.bam]
bamdamage [-m qual] [-b qual] [-s name] [file.bam]
bamdamage generates plots for the read length distribution, damage distribution, 5' damage pattern, 3' damage pattern in ine pdf-file. The input is a single bam file either on the command line or given on standard input (stdin).
Skip reads with mapping quality smaller than qual. Default: 30.
Skip bases with base quality smaller than qual. Default: 20.
Use name for the legend in plots. Default is the file name.
Generate AustralianAborigine_300000.pdf with the sample labeled Aborgine.
bamdamage AustralianAborigine_300000.bam -s Aborgine
When using bamdamage for a publication please cite:
<<INSERT ARTICLE HERE>>
Copyright (C) 2013,2014 Yong Wang <waterwy@gmail.com> and Ole Tange <bamdamage@tange.dk>.
bamdamage will exit with non-zero status if it discovers anything is wrong.
Report bugs to <bamdamage@tange.dk>.
Copyright (C) 2013,2014 Free Software Foundation, Inc.
This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or at your option any later version.
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bamdamage uses Perl, R, and samtools.
bammds(1), samtools(1), R(1)