.TH BAM_RMDUP_COLLAPSED "1" "February 2017" "bam_rmdup_collapsed 1.2.7" "User Commands"
.SH NAME
bam_rmdup_collapsed \- filter BAM file for PCR duplicates
.SH SYNOPSIS
.B paleomix rmdup_collapsed
[options] < sorted.bam > out.bam
.SH DESCRIPTION
The rmdup_collapsed filters a BAM file for PCR duplicates unpaired reads under
the assumption that any unpaired read have been generated by the merging of
overlapping paired\-end reads, and thereby represent the complete template
sequence. PCR duplicates are therefore detected based on both the 5' and 3'
alignment coordinate.
.PP
Paired reads (0x1), unmapped reads (0x4), secondary alignments (0x100),
reads that failed QC (0x200), and chimeric alignments (0x800), as identified
using the BAM record flags, are not filtered, but simply written to the output.
.PP
By default, filtered reads are flagged using the "duplicate" flag (0x400), and
written to the output. Use the \fB\-\-remove\-duplicates\fR command\-line option to
instead remove these records from the output.
.PP
This program is part of the paleomix(1) suite.
.SH OPTIONS
.SS "positional arguments:"
.TP
input
BAM file; if not set, input is read from STDIN.
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-\-remove\-duplicates\fR
Remove duplicates from output; by default duplicates
are only flagged (flag = 0x400).
.TP
\fB\-\-seed\fR SEED
Seed used for randomly selecting representative reads
when no reads have quality scores assigned[default:
initialized using system time].
.SH SEE ALSO
paleomix(1)
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.