BAM2STARCH_SLURM(1)

💖 BAM2STARCH_SLURM(1) 💖

okay bestie, so you know how we're always like "ugh I have an indexed BAM file and I just want a sorted BED file but I don't wanna do it on my sad little laptop"?? yeah. this is that. this is the manual page for bam2starch_slurm, version 2.4.42+dfsg. sit down, grab a strawberry, we're doing cluster things 🍓✨

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🌈 SYNOPSIS 🌈

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

(and yes, that literally says bam2bed_slurm in the synopsis even though the page is about bam2starch_slurm — I'm not fixing it, that's canon, iykyk 💅)

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✨ DESCRIPTION ✨

okay so the whole vibe here: you hand over the name of an indexed BAM file, and it makes you a sorted BED file — but it does it using the cluster. not your poor overheating laptop. the cluster. 👑

bestie note: stdin isn't supported through this wrapper script. so don't even try to pipe into it, it's not giving that today 😭

you can also throw in --clean, and it'll remove <input-indexed-bam-file> right after it's been turned into BED. like, gone gone. poof. so make sure you're done with it, fr fr 💀

and guess what — you can pass in the name of the output bed archive you want created. it's your call, main character. 🌸 otherwise? it just does the lazy-chic thing and names the output after the input file, with an extra

'.bed' ending tacked on the end.

and if your input file ends with '.bam', that gets stripped off first. cute little makeover, no notes. 💅✨

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🫶 SEE ALSO 🫶

so like, the full documentation for bam2starch_slurm lives as a Texinfo manual — yes, Texinfo, she's vintage, she's iconic 👑

and if the info and bam2starch_slurm programs are properly installed at your site (fingers crossed 🤞), then this command:

info bam2starch_slurm

should give you access to the complete manual. that's it. that's the gateway. go forth. 🦋

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and that's the whole page bestie!! 🎀 this is bam2starch_slurm version 2.4.42+dfsg, dated August 2025 — slay, stan, no cap, periodt 💖✨🌸