CNVKIT-REFERENCE2TARGETS(1)

✨ NAME ✨

cnvkit-reference2targets — the little icon that pulls your target and antitarget BED files straight out of a CNVkit reference file 🎀

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🌸 DESCRIPTION 🌸

okay so first things first, here's the vibe of how you actually run this thing:

usage: cnvkit-reference2targets [-h] [-o OUTPUT] reference

So what's the tea? Bestie, this script extracts target and antitarget BED files from a CNVkit reference file. That's it, that's the whole job, and it does it flawlessly 💅

Now here's the part where it gets useful. Once you've got a stable CNVkit reference for your platform — like, locked in, committed, no notes — you can use this script to drop the "bad" bins from your target and antitarget BED files. Why do you care? Because then you're not out here unnecessarily calculating coverage in those bins during future runs. Wasted compute? Not on our watch. Not today. 🚫

And it's got a second little superpower, because of course it does: this script is also useful to recover the target and antitarget BED files that match the reference — for when those BED files are missing, or when you're sitting there like "bestie which one of these is the correct one?? 😭". Yeah. It's got you. 🫶

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🎯 positional arguments:

• reference — the reference file. Your whole reference. The main character, honestly. 👑

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💖 optional arguments:

• -h, --help — shows this help message and then dips. classic. shows help, exits, no drama. ✨
• -o OUTPUT, --output OUTPUT — the output base name. And here's the cute part: extensions are added automatically, so don't you dare add them yourself, she'll handle it. 🌈

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👑 that's the whole page, bestie

You just read the manual for cnvkit-reference2targets, version 0.9.9, dated October 2021. Go forth and recover those BED files. Slay 💅🌸✨