WCFST(1)

✨ WCFST(1) ✨ — aka wcFst, the wcFst (VCF statistics) era 💖

okay bestie, sit down, hydrate, because this one is a whole moment. This is the manual page for wcFst, and yes it's filed under section 1 of the manual, so it's a user command. Let's get into it 🫶

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🎀 NAME 🎀

wcFst — that's it, that's the name, short and iconic 💅

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🦋 SYNOPSIS 🦋

wcFst –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

(yes those are the real dashes, do not come for me, copy it exactly as written 🙈)

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🌸 DESCRIPTION 🌸

wcFst is Weir & Cockerham's Fst, computed for two populations. That's the whole vibe. 🔥

Now here's the part everyone gets weird about: negative values are VALID. Not a bug, not a glitch, not your pipeline being messy. They're sites that can be treated as zero Fst. Periodt. 💯

Want the lore? Go read Evolution, Vol. 38 N. 6 Nov 1984. Specifically, wcFst uses equations 1, 2, 3, 4. iykyk 📖

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💅 OPTIONS 💅

Output : 3 columns :

...okay so the doc says 3 columns and then lists five things, and we're just going to accept that as part of its charm 💀 anyway:

1. seqid
2. position
3. target allele frequency
4. background allele frequency
5. wcFst

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• t, target — required ✋ argument: a zero based comma separated list of target individuals, corrisponding to VCF columns. Like, zero-based, bestie, do not count from one, I'm begging 🥺
• b, background — required ✋ argument: a zero based comma separated list of background individuals, corrisponding to VCF columns.
• f, file — required ✋ argument: a properly formatted VCF. Feed it right or it will simply not eat 🍓
• y, type — required ✋ argument: the genotype likelihood format; options are genotype : GT, GL, PL, GP. Pick one, pick wisely 👑
• r, region — optional ✨ argument: a tabix compliant genomic range: seqid or seqid:start-end
• d, deltaaf — optional ✨ argument: skip sites where the difference in allele frequencies is less than deltaaf, default is zero. So if you leave it alone, nothing gets skipped 🎀

Type: statistics

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🌈 EXIT VALUES 🌈

• 0 — Success 🎉 slay, it worked
• not 0 — Failure 😭 something went sideways

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🔥 SEE ALSO 🔥

• vcflib(1)

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💜 OTHER 💜

(the catch-all corner of the page, we love her)

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 thing, bestie 💖 this page comes to you from the vcflib source, and it's the wcFst page, living its best life in section 1 of the manual. go forth and compute Fst responsibly 🧚✨