CNVKIT_REFERENCE(1)

✨ NAME ✨

cnvkit_reference — okay bestie, this is the little icon that compiles a coverage reference out of the files you hand it, and those files are your normal samples. That's the whole vibe. 💖

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🎀 DESCRIPTION 🎀

so like, here's literally how you invoke her:

cnvkit.py reference [-h] [-f FASTA] [-o FILENAME] [-c] [--min-cluster-size NUM] [-x {m,y,male,Male,f,x,female,Female}] [-y] [-t TARGETS] [-a ANTITARGETS] [--no-gc] [--no-edge] [--no-rmask] [references ...]

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🌸 positional arguments 🌸

• references — your normal-sample target or antitarget .cnn files, or the directory that's holding all of them. she'll find them, don't worry. 🫶

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💅 options 💅

• -h, --help — shows this help message and then dips. classic. ✌️
• -f FASTA, --fasta FASTA — the reference genome, in FASTA format (think UCSC hg19.fa). 🧬
• -o FILENAME, --output FILENAME — what you wanna name the output file. name it something cute, she deserves it. 💾
• -c, --cluster — calculates and stores summary stats for clustered subsets of the normal samples that have similar coverage profiles. like she's grouping the girlies by vibe. 👯
• --min-cluster-size NUM — the minimum cluster size to keep in the reference profiles. [Default: 4] — no tiny friend groups allowed. 🙅
• -x {m,y,male,Male,f,x,female,Female}, --sample-sex {m,y,male,Male,f,x,female,Female}, -g {m,y,male,Male,f,x,female,Female}, --gender {m,y,male,Male,f,x,female,Female} — tells her the chromosomal sex of all the samples you're giving her, as male or female. (Default: guess each sample from coverage of X and Y chromosomes) — yeah she's guessing if you don't say, so maybe just say. 😭
• -y, --male-reference, --haploid-x-reference — creates a male reference: it shifts female samples' chrX log-coverage by -1, so the reference chrX average comes out to -1. Otherwise she shifts male samples' chrX by +1, so the reference chrX average is 0. pick a lane, bestie. ⚖️

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To construct a generic, flat" copy number reference with neutral expected coverage:"

ngl that line in the original is a whole mood, but the point is: this is the mode where you want a plain, flat reference with neutral expected coverage. 🫧

• -t TARGETS, --targets TARGETS — the target intervals (.bed or .list). 🎯
• -a ANTITARGETS, --antitargets ANTITARGETS — the antitarget intervals (.bed or .list). the little side quests. 🌈

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To disable specific automatic bias corrections:

iykyk — sometimes the auto-corrections are doing too much and you gotta turn them off yourself. 🙈

• --no-gc — skips GC correction. ✂️
• --no-edge — skips edge-effect correction. 🚫
• --no-rmask — skips RepeatMasker correction. 💀

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and that's the whole page, bestie, no cap. this was version 0.9.10, dated July 2023, and yeah the manual name is literally CNVKIT_REFERENCE(1) so now you know it fr fr. go compile something iconic. 👑💖✨