BAM_RMDUP_COLLAPSED(1)

💖 BAM_RMDUP_COLLAPSED 💖

okay bestie, welcome to the bam_rmdup_collapsed page from the User Commands section of the manual — she's a whole vibe and she's here to clean up your BAM file ✨

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🌸 NAME 🌸

bam_rmdup_collapsed — filter BAM file for PCR duplicates 💅

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🎀 SYNOPSIS 🎀

paleomix rmdup_collapsed [options] < sorted.bam > out.bam

like… that's it. that's the whole summoning ritual 🪄

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🦋 DESCRIPTION 🦋

okay so here's the tea ☕: rmdup_collapsed filters a BAM file for PCR duplicates in unpaired reads, and it does this under one very specific assumption — that any unpaired read was generated by the merging of overlapping paired-end reads, and therefore represents the complete template sequence. no cap, that's the whole premise. 🧚

so because of that, PCR duplicates get detected based on both the 5' and 3' alignment coordinate. both ends. she's thorough like that. 👑

and listen — some reads just do NOT get filtered, they get a free pass and are simply written straight to the output. who are these VIPs? 🎟️

• Paired reads (0x1)
• unmapped reads (0x4)
• secondary alignments (0x100)
• reads that failed QC (0x200)
• chimeric alignments (0x800)

all identified using the BAM record flags. they're not filtered, bestie, they just vibe through to the output. 💫

by default, the reads that do get filtered are flagged using the "duplicate" flag (0x400) and written to the output. but if you want them GONE gone? use the --remove-duplicates command-line option and those records get yeeted from the output entirely. 🗑️✨

this program is part of the paleomix(1) suite 🫶

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✨ OPTIONS ✨

💜 positional arguments:

• input — BAM file; if it's not set, input is read from STDIN. she's flexible like that 💅

💖 optional arguments:

• -h, --help — show this help message and exit. iconic behavior honestly 😌
• --remove-duplicates — Remove duplicates from output; by default duplicates are only flagged (flag = 0x400). so like, if you're tired of seeing them, this is your moment 🫶
• --seed SEED — Seed used for randomly selecting representative reads when no reads have quality scores assigned [default: initialized using system time]. so yeah, if nobody has a quality score, she's just gonna pick a rep at random — and the seed controls that randomness. default is literally the system clock ⏰🎲

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👀 SEE ALSO 👀

• paleomix(1)

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🌈 AUTHOR 🌈

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. slay, Andreas 💖

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and that's the whole page bestie!! 🌸💖✨ this is bam_rmdup_collapsed version 1.2.7, dated February 2017 — old but iconic, fr fr. now go forth and deduplicate responsibly 🧚‍♀️💅🦋