CNVKIT_CALL(1)

💖 CNVKIT_CALL(1) 💖

okay bestie, gather round, because this is cnvkit_call — the part of the CNVkit fam that actually calls copy number variants from segmented log2 ratios. it's giving "the glow-up at the end of the pipeline" ✨

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✨ NAME ✨

cnvkit_call — call copy number variants from segmented log2 ratios. no cap, that's the whole job. 🎀

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🌸 DESCRIPTION 🌸

so the usage is literally this, and yes it's long, she's a big girl:

cnvkit.py call [-h] [--center [{mean,median,mode,biweight}]]
        [--center-at CENTER_AT] [--filter {ampdel,cn,ci,sem}]
        [-m {threshold,clonal,none}] [-t THRESHOLDS] [--ploidy PLOIDY]
        [--purity PURITY] [--drop-low-coverage] [-x
        {m,y,male,Male,f,x,female,Female}] [-y] [-o FILENAME] [-v
        FILENAME] [-i SAMPLE_ID] [-n NORMAL_ID] [--min-variant-depth
        MIN_VARIANT_DEPTH] [-z [ALT_FREQ]] filename

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🫶 positional arguments

• filename — the copy ratios file. she takes .cnr or .cns. that's the input, that's the vibe. 💜

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🦋 options

• -h, --help — show this help message and exit. the classic. the icon. the "help me help you". 🙈
• --center [{mean,median,mode,biweight}] — re-centers your log2 ratio values using this estimator of the center / average value. and if you pass it with no argument? it uses 'median'. she has a default and she's confident about it. 💅
• --center-at CENTER_AT — subtracts a constant number from all the log2 ratios. this is for "manual" re-centering, i.e. when the --center option is giving you unsatisfactory results. it's the "fine, I'll do it myself" option. 😭
• --filter {ampdel,cn,ci,sem} — merges segments flagged by the specified filter(s) with the adjacent segment(s). cleaning up the friend group, basically. 🧚
• -m {threshold,clonal,none}, --method {threshold,clonal,none} — the calling method. [Default: threshold] ⭐
• -t THRESHOLDS, --thresholds THRESHOLDS — hard thresholds for calling each integer copy number, separated by commas. use the = sign on the command line, e.g.: -t=-1,0,1. [Default: -1.1,-0.25,0.2,0.7] — note that = bestie, it's not optional vibes, it's required. 💀
• --ploidy PLOIDY — ploidy of the sample cells. [Default: 2] 👑
• --purity PURITY — estimated tumor cell fraction, a.k.a. purity or cellularity. two names, one option, she contains multitudes. 🌈
• --drop-low-coverage — drops very-low-coverage bins before segmentation, so you don't get false-positive deletions in poor-quality tumor samples. protective queen behavior. 🫶
• -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} — specify the sample's chromosomal sex as male or female. (otherwise it's guessed from X and Y coverage, which is honestly kind of iconic of it.) ✨
• -y, --male-reference, --haploid-x-reference — was a male reference used? if so, expect half ploidy on chrX and chrY; otherwise, only chrY has half ploidy. and in CNVkit specifically: if a male reference was used, the "neutral" copy number (ploidy) of chrX is 1; chrY is haploid for either reference sex. yes this is confusing, yes it's real, yes you need to know it. 🔥
• -o FILENAME, --output FILENAME — output table file name (a CNR-like table of segments, .cns). 💖

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💅 to additionally process SNP b-allele frequencies for allelic copy number:

like, if you wanna go deeper and do the allelic thing too, these are your girls:

• -v FILENAME, --vcf FILENAME — VCF file name containing variants for calculation of b-allele frequencies. 🌸
• -i SAMPLE_ID, --sample-id SAMPLE_ID — name of the sample in the VCF (-v/--vcf) to use for b-allele frequency extraction. 🎀
• -n NORMAL_ID, --normal-id NORMAL_ID — corresponding normal sample ID in the input VCF (-v/--vcf). this sample is used to select only germline SNVs to calculate b-allele frequencies. she's the control, respect her. 🦋
• --min-variant-depth MIN_VARIANT_DEPTH — minimum read depth for a SNV to be used in the b-allele frequency calculation. [Default: 20] ⭐
• -z [ALT_FREQ], --zygosity-freq [ALT_FREQ] — ignore the VCF's genotypes (the GT field) and instead infer zygosity from allele frequencies. [Default if used without a number: 0.25] — so you can just yeet -z in there and she'll handle it. 💜

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⚠️ reminder bestie: copy the option names and values exactly as written. these flags are picky and the = in -t is not a suggestion, it's the law. 💀

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👑 sign-off 👑

this was cnvkit.py call 0.9.10, from July 2023, and the manual page you're reading is CNVKIT_CALL(1). that's the whole thing, you ate, go call some copy numbers. 🍓✨💖