CNVKIT_FIX(1)

✨ CNVKIT_FIX — the cnvkit_fix(1) page, bestie edition 💖

okay so this is a User Commands manual, and it's literally called cnvkit_fix. Let's get into it 🫶

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🌸 NAME 🌸

cnvkit_fix — Combine target and antitarget coverages and correct for biases.

Adjust raw coverage data according to the given reference, correct potential biases and re-center. iconic behavior tbh 💅

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🦋 DESCRIPTION 🦋

So here's the whole vibe of how you call it:

usage: cnvkit.py fix [-h] [-c] [-i SAMPLE_ID] [--no-gc] [--no-edge] [--no-rmask] [-o FILENAME] target antitarget reference

That's the shape of it. Now let's break down every single piece, no skipping, we're thorough in this house 👑

🌈 positional arguments (the ones you have to give it)

• target — the Target coverage file (.targetcoverage.cnn). 🎯
• antitarget — the Antitarget coverage file (.antitargetcoverage.cnn). 🚫🎯
• reference — the Reference coverage (.cnn). 📖

🎀 options (the lil extras, all optional, all slay)

• -h, --help — show this help message and exit. the classic escape hatch 🙈
• -c, --cluster — Compare and use cluster-specific values present in the reference profile. (Requires that the reference profile was built with the --cluster option.) ⚠️ so like, don't skip the parenthetical, it's giving "you must have done the homework first" ✨
• -i SAMPLE_ID, --sample-id SAMPLE_ID — Sample ID for target/antitarget files. Otherwise inferred from file names. 🏷️ if you don't tell it, it'll guess from the filenames, no cap
• --no-gc — Skip GC correction. 💀
• --no-edge — Skip edge-effect correction. 💀
• --no-rmask — Skip RepeatMasker correction. 💀
• -o FILENAME, --output FILENAME — Output file name. 📝

fr fr, all three of those --no-* flags are literally just "turn the correction off" — if you use them, you are choosing not to correct for that thing. Just so we're clear 🫶

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and that's the whole page, bestie. no gatekeeping, every flag accounted for 🧚

this little manual is from cnvkit.py fix, version 0.9.10, dated July 2023 — periodt, that's the sign-off, mwah 💖✨🎀