bam_rmdup_collapsed1
Filter bam file for pcr duplicates
Usage
paleomix rmdup_collapsed
[options]
<
sorted.bam
>
out.bam
Overview
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.
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.
Options
positional arguments:
- input
-
BAM file; if not set, input is read from STDIN.
optional arguments:
-
-h, --help -
show this help message and exit
-
--remove-duplicates -
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 time].
Releases
Unchanged in 4 releases since Debian 10 (Buster).