BAM2BED_SLURM(1)

📦
version 2.4.42 · 2 versions
, in ubuntu resolute, ubuntu stonking

💖 BAM2BED_SLURM 💖

okay bestie, welcome to bam2bed_slurm — it's a User Command, it's part of the bam2bed_slurm 2.4.42+dfsg era, and it is literally about to turn your BAM into a BED while the cluster does the heavy lifting. no cap. 🦋

✨ SYNOPSIS ✨

bam2bed_slurm [--help] [--clean] <input-indexed-bam-file> [output-bed-file]

🌸 DESCRIPTION 🌸

okay so here's the vibe: you hand it the name of an indexed BAM file, and it makes you a sorted BED file — and it does it using the cluster. main character energy fr fr 👑

🚨 important: stdin isn't supported through this wrapper script. like, at all. don't even try it. 😭

drop --clean in there and it will remove <input-indexed-bam-file> after turning it into BED. yes, gone. deleted. make sure you meant that. 💀

you can also pass in the name of the output bed archive you want created — your call, your naming era. 🎀

but if you don't? no worries, it's giving autopilot: the output gets the same name as the input file, with an additional

.bed

ending tacked on. and if the input file already ends with .bam, that part gets stripped off. slay. ✨

👀 SEE ALSO 👀

the full documentation for bam2bed_slurm is maintained as a Texinfo manual. if the info and bam2bed_slurm programs are properly installed at your site, then this command

info bam2bed_slurm

should give you access to the complete manual. iykyk 📖💅

and that's the whole page, bestie — this was bam2bed_slurm version 2.4.42+dfsg, dated August 2025. go forth and convert. 🌈💖

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