BAM2BED_SGE(1)

✨ bam2bed_sge(1) ✨

okay bestie, sit down, hydrate, because this one is so useful. we're in the User Commands section of the manual, and this is the page for bam2bed_sge — the cluster-powered glow-up that turns your BAM into a BED. no cap.

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🎀 NAME 🎀

bam2bed_sge — literally the manual page for bam2bed_sge version 2.4.42+dfsg. that's it, that's the name. iconic of her honestly.

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🌸 SYNOPSIS 🌸

bam2bed_sge [--help] [--clean] <input-indexed-bam-file> [output-bed-file]

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🦋 DESCRIPTION 🦋

okay so the whole vibe is: you hand over the name of an indexed BAM file, and she creates a sorted BED file for you — and she does it using the cluster. main character energy, truly. she's not doing this alone, she's got the whole cluster behind her. 💅

not me having to say this: stdin is NOT supported through this wrapper script. sorry babe, no piping into her. she wants a real file name, not a stream. 🙈

if you want her to be a little ruthless, add --clean — that makes her remove <input-indexed-bam-file> after she's turned it into BED. gone. deleted. she ate and left no crumbs. 😭 (obviously, only do this if you're sure, because that input file does not come back.)

you can also pass in the name of the output bed archive you want her to create. if you do, slay, that's your output name. if you don't? she picks one for you:

• the output gets the same name as the input file, plus an extra .bed ending
• and if the input file ends with .bam, that .bam gets stripped off first

so yes, she's doing the naming math for you, you don't have to lift a finger. 🫶

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🌈 SEE ALSO 🌈

the full documentation for bam2bed_sge is maintained as a Texinfo manual. if the info and bam2bed_sge programs are properly installed at your site, this command:

info bam2bed_sge

should give you access to the complete manual. go read it, it's giving thorough. 📖✨

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and that's the whole page, bestie! this was bam2bed_sge version 2.4.42+dfsg, from August 2025 — she's fresh, she's current, she's in her era. now go convert something. 💖