CNVKIT_SEX(1)

💖 cnvkit_sex — the manual, but make it a vibe 💖

okay so bestie, you found the CNVKIT_SEX(1) page (it lives in the User Commands section, very demure, very mindful) and honestly? it's a short one, so we're gonna get you fully caught up before your coffee even cools. 🎀

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✨ NAME ✨

cnvkit_sex — guess what sex your samples are, by peeking at the relative coverage of chromosomes X and Y. that's it. that's the whole job. 👑

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🌸 DESCRIPTION 🌸

so the way you actually run this is:

usage: cnvkit.py sex [-h] [-y] [-o FILENAME] filenames [filenames ...]

and here's the breakdown, babes. 💅

🫶 positional arguments:

• filenames — one or more files, bestie. these are your copy number or copy ratio files, and they come with the extensions *.cnn or *.cnr. that's the whole input situation. drop 'em in. 🌈

🦋 options:

• -h, --help — shows this help message and then dips. classic. 💀
• -y, --male-reference, --haploid-x-reference — okay this one's the plot twist. turn this on if you already know your inputs were normalized against a male reference. what that means: female samples will end up with +1 log-coverage of chrX. and if you don't do this, the flip side is that male samples would have -1 chrX. so like, pick your reference, know your reference, no cap. 🧚
• -o FILENAME, --output FILENAME — names the output table file. give it a FILENAME, get a table. iconic. ✨

ngl bestie, that's genuinely the whole page. no sneaky extra flags hiding in here. i checked. twice. 🍓

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💜 a lil sign-off, because you deserve it 💜

this page is from cnvkit.py sex version 0.9.10, and it was dated July 2023 — so like, a lil vintage, still slaying. go forth and sex your samples (chromosomally. chromosomally!!! 😭). mwah. 🫶🌸⭐