CNVKIT_TARGET(1)

💖 CNVKIT_TARGET 💖

okay bestie, so this is the cnvkit_target manual page — it lives in the User Commands section of your friendly neighbourhood manual, and it's all about turning bait intervals into targets that CNVkit actually vibes with. slay.

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✨ NAME ✨

cnvkit_target — transform bait intervals into targets more suitable for CNVkit. that's it, that's the whole job. iconic behaviour honestly 💅

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🌸 DESCRIPTION 🌸

here's how you call it, fr fr:

cnvkit.py target [-h] [--annotate ANNOTATE] [--short-names] [--split]

[-a AVG_SIZE] [-o FILENAME]
       interval

yes the line breaks are doing their own little thing, we don't question the usage string, we just respect it 🫶

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🎀 positional arguments 🎀

• interval — a BED file or interval file that lists the targeted regions. basically: tell it where you're aiming, bestie 🎯

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💜 options 💜

• -h, --help — shows this help message and then dips. classic. exit stage left ✨
• --annotate ANNOTATE — use gene models from this file to assign names to the target regions. format-wise it wants a UCSC refFlat.txt or ensFlat.txt file (preferred, the main character energy option 💅), or a BED, interval list, GFF, or something similar. no cap, it's flexible but it has favourites.
• --short-names — reduces multi-accession bait labels so they're short and consistent. glow-up for your labels, they were doing too much 🌈
• --split — splits large tiled intervals into smaller, consecutive targets. chopping the big ones down into bite-size pieces 🍓
• -a AVG_SIZE, --avg-size AVG_SIZE — the average size of split target bins. heads up though: results are approximate, so don't come for it if the bins aren't exactly this size, it literally told you 😭

default is 266.6666666666667 — yes, that is the actual default, and yes, that many sixes is giving cursed-but-fabulous 🔥

• -o FILENAME, --output FILENAME — the output file name. where your gorgeous results get written 💖

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💀 reminder bestie: --avg-size results are approximate. that's in the original, that's not me being dramatic, that's just the truth.

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and that's the whole page, periodt. this was cnvkit.py target 0.9.10, dated July 2023 — written down here in the cnvkit_target(1) manual page. go forth and target some regions, you absolute genius 🦋✨👑