CNVKIT_BREAKS(1)

💖 CNVKIT_BREAKS 💖

okay so this is cnvkit_breaks, bestie — it lives in section 1 of the User Commands manual, and it's here to help you find the targeted genes where a copy number breakpoint is happening. like, where does the DNA go off the rails? this page tells you. ✨

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🌸 NAME 🌸

cnvkit_breaks — list the targeted genes in which a copy number breakpoint occurs. no cap, that's the whole job and she does it beautifully. 💅

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🦋 DESCRIPTION 🦋

here's the vibe, the literal invocation:

usage: cnvkit.py breaks [-h] [-m MIN_PROBES] [-o FILENAME] filename
       segment

okay so that's the shape of it. now let's break down every single piece because we do not skip details in this house. 🫶

🎀 positional arguments: 🎀

• filename — the processed sample coverage data file (*.cnr), which is what the fix sub-command spits out. that's your starting material, bestie.
• segment — the segmentation calls (.cns), aka the output of the segment command. yep, this one right here.

✨ options: ✨

• -h, --help — show this help message and exit. the classic. the icon. when in doubt, ask for help. 👑
• -m MIN_PROBES, --min-probes MIN_PROBES — the minimum number of within-gene probes on both sides of a breakpoint for it to get reported. so if it doesn't clear the bar on both sides, it's not making the list. [Default: 1]
• -o FILENAME, --output FILENAME — output table file name. that's where your results go. 📝

heads up: -m needs probes on both sides of the breakpoint, not just one. the default is 1, so out of the box pretty much everything reports. turn it up if you want only the confident ones. 🌈

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and that's the whole page, fr fr. no filler, no skips, every flag accounted for. 💜

this gem is cnvkit.py breaks 0.9.10, dated July 2023 — go forth and find those breakpoints, main character. 💖🦋✨🎀🌸💅🫶