PFST(1)

✨ PFST(1) — like, the pFst page, bestie 💅

okay so this is the manual page for pFst, from the pFst (VCF statistics) crew 🧚 sit down, grab a strawberry, we're doing allele frequencies today 🍓

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🌸 NAME 🌸

pFst — no cap, that's the whole name 💖

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🦋 SYNOPSIS 🦋

pFst –target 0,1,2,3,4,5,6,7 –background 11,12,13,16,17,19,22 –file
my.vcf –deltaaf 0.1 –type PL

like. that's it. that's the vibe check ✅

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💜 DESCRIPTION 💜

pFst is a probabilistic approach for detecting differences in allele frequencies between two populations. literally what it says on the tin, periodt 👑

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✨ OPTIONS ✨

pFst is a likelihood ratio test (LRT) quantifying allele frequency differences between populations. okay so here's the tea, bestie:

• by default the LRT uses the binomial distribution 🎀
• if Genotype likelihoods are provided it uses a modified binomial that weights each allele count by its certainty (so it's like, the binomial but it knows how sure it is, iconic) 💅
• if type is set to 'PO' the LRT uses a beta distribution to fit the allele frequency spectrum of the target and background. PO requires the AD and DP genotype fields and requires at least two pools for the target and background 🫶
• the p-value calculated in pFst is based on the chi-squared distribution with one degree of freedom 🌈

Output : 3 columns : (yes, exactly three, no extras, we're minimal here)

1. seqid
2. position
3. pFst probability

now the flags, and there are a lot of them, so lock in 🔥

• -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. (emphasis on properly, bestie, we will know) 📄
• -y, --type — required. argument: genotype likelihood format ; genotypes: GP, GL or PL; pooled: PO 🧬
• -d, --deltaaf — optional. argument: skip sites where the difference in allele frequencies is less than deltaaf, default is zero 🚫
• -r, --region — optional. argument: a tabix compliant genomic range : seqid or seqid:start-end 🗺️
• -c, --counts — optional. switch : use genotype counts rather than genotype likelihoods to estimate parameters, default false 🔁

Type: statistics 📊

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💀 EXIT VALUES 💀

• 0 — Success 🥳
• not 0 — Failure 😭

not me checking exit codes like they're a text from my crush. 0 means they replied. not 0 means. yeah. 🙈

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👑 SEE ALSO 👑

vcflib(1) — go read that one too, it's giving connected universe 🦋

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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!! this one shipped as pFst (vcflib) — that's the source/version tag living down in the footer, and the page itself is dated PFST(1) up top like a lil timestamp on the whole thing 🫶 ily, go genotype something responsibly ✨💅🎀