bam_rmdup_collapsed - filter BAM file for PCR duplicates
[options] < sorted.bam > out.bam
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'
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.
By default, filtered reads are flagged using the "duplicate" flag
(0x400), and written to the output. Use the --remove-duplicates
command-line option to instead remove these records from the output.
This program is part of the paleomix(1) suite.
- BAM file; if not set, input is read from STDIN.
- -h, --help
- show this help message and exit
- Remove duplicates from output; by default duplicates are
only flagged (flag = 0x400).
- --seed SEED
- Seed used for randomly selecting representative reads when
no reads have quality scores assigned[default: initialized using system
This manpage was written by Andreas Tille for the Debian distribution and can be
used for any other usage of the program.