BAMFILTERRG.PY(1)

💖 BAMFILTERRG.PY(1) 💖

User Commands · bamfilterrg.py · bestie edition ✨

✨ NAME ✨

bamfilterrg.py — filter readgroup(s) from a BAM file 🧬💅

🌸 SYNOPSIS 🌸

bamfilterrg.py [-h] [-i BAM] [-r STR] [-n INT] [-S] [-b] [-u]

🦋 DESCRIPTION 🦋

okay so. you have a BAM file. it's got readgroups in it. some of those readgroups you want, some you don't. this script is the bouncer at the door — filter readgroup(s) from a BAM file. that's it, that's the whole vibe. no cap. 💖

👑 OPTIONS 👑

🎀 optional arguments:

• -h, --help — show this help message and exit. the classic. the icon. when in doubt, ask for help 🫶
• -i BAM, --input BAM — Input BAM file. this is the file you're filtering, your main character, the whole reason we're here 🌟
• -r STR, --readgroup STR — Read group(s) to extract (comma separated). yes bestie, plural — you can list several and comma them apart 💖
• -n INT — Output first n alignments and quit. just a lil taste. a snack. n alignments and then we're out 🍓
• -S — Input is SAM format. heads up, this changes what you're feeding it — not a BAM, a SAM 📄
• -b — Output BAM format. because sometimes you want it bammed back up 🎁
• -u — Output uncompressed BAM format (implies -b). notice how it implies -b — so you don't gotta say both, it already knows 💅

💜 AUTHOR 💜

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. we love a humble legend 🫶✨

that's the whole page bestie, go filter some readgroups and slay 🌈💖

bamfilterrg.py 0.0.1+git2017041... · June 2020 · mwah, bye!! 👑💅