PVST(1)

💖 pVst — like, the manual page, but make it make sense 💖

okay bestie, welcome to pVst(1) — yeah, that's the section 1 manual, and the whole vibe is pVst (VCF statistics). sit down, grab a boba, we're doing copy-number math and we're gonna enjoy it 🧋✨

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✨ NAME ✨

pVst — that's it, that's the name, she's short, she's iconic, she does one thing 👑

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🌸 SYNOPSIS 🌸

pVst –target 0,1,2,3,4,5,6,7 –background 11,12,13,16,17,19,22 –file
my.vcf –type CN

literally just hand her some individuals, a background, a VCF, and a field name, and she goes 🦋

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💅 DESCRIPTION 💅

so pVst calculates vst, which is a measure of CNV stratification. that's the whole job. no cap.

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🎀 OPTIONS 🎀

first, the lore behind the number, because you deserve context, bestie 🫶

the statistic Vst is used to test the difference in copy numbers at each SV between two groups:

Vst = (Vt-Vs)/Vt

where Vt is the overall variance of copy number and Vs the average variance within populations.

Output : 4 columns :

1. seqid
2. position
3. end
3. vst
4. probability

not me renumbering the original page 💀 i'm not touching it — those are the numbers it shipped with, and we respect the source material. four columns, five lines, that's just how she is 🙈

now the actual flags, one bullet each, no skipping, we don't do that here:

• -t, --target — required — argument: a zero based comma separated list of target individuals corresponding to VCF columns
• -b, --background — required — argument: a zero based comma separated list of background individuals corresponding to VCF columns
• -f, --file — required — argument: a properly formatted VCF.
• -y, --type — required — argument: the genotype field with the copy number: e.g. CN|CNF
• -r, --region — optional — argument: a tabix compliant genomic range : seqid or seqid:start-end
• -x, --cpu — optional — argument: number of CPUs [1]
• -n, --per — optional — argument: number of permutations [1000]

Type: statistics 📊

reminder that -t, -b, -f and -y are required, so if you skip one and then act shocked when it fails... bestie, that's on you 😭

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🌈 EXIT VALUES 🌈

• 0 — Success 🎉 (the good ending)
• not 0 — Failure 💀 (the other ending)

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⭐ SEE ALSO ⭐

• vcflib(1)

go read your other manuals, i'll wait 🫶

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🧚 OTHER 🧚

👑 LICENSE 👑

Copyright 2011-2024 (C) Erik Garrison and vcflib contributors. MIT licensed. Copyright 2020-2024 (C) Pjotr Prins.

🍓 AUTHORS 🍓

Erik Garrison and vcflib contributors.

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and that's the whole page, bestie — pVst (vcflib), straight out of the vcflib crew, no date on the footer so don't come for me about one 💖✨ mwah, go stratify some CNVs, you absolute main character 🦋