VCFLD(1)

👑 VCFLD(1) — the vcfld page, aka VCF transformation vibes

okay bestie, so this is the manual page for vcfld — she lives in the vcfld (VCF transformation) corner of the manual-verse and she is so ready to compute LD with you. pull up a chair, grab a boba 🧋, and let's get into it.

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✨ NAME ✨

vcfld — that's her. that's the name. short, sweet, iconic, no notes. 💅

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✨ SYNOPSIS ✨

here's how you call her, literally character for character, don't @ me:

vcfld –target 0,1,2,3,4,5,6,7 –background 11,12,13,16,17,19,22 –file
my.vcf -e -d -r

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✨ DESCRIPTION ✨

Compute LD. that's the whole description. she said what she said. 💖

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✨ OPTIONS ✨

okay so this is the part where you actually have to pay attention. some of these are required, which means no they're not optional, bestie, I don't make the rules. 🫶

• t,target — required 🌸 argument: a zero base comma separated list of target individuals corresponding to VCF columns. zero base means you start counting at 0, not 1, and yes that trips everyone up, it's fine, it's giving classic bioinformatics.
• b,background — required 🌸 argument: a zero base comma separated list of background individuals corresponding to VCF columns. same deal, zero base, comma separated, columns from the VCF. 💜
• f,file — required 🌸 argument: a properly formatted phased VCF file. key word being phased, and key word being properly formatted, she is not going to hold your hand on this one. 😭
• y,type — required 🌸 argument: type of genotype likelihood, and your choices are PL, GL or GP. pick one. just one. 🎀
• w,window — optional ✨ argument: window size to average LD. the default is 1000, so if you say nothing she's rolling with a thousand. no cap.
• e,external — optional ✨ switch: population to calculate LD expectation. the default is target. it's a switch, so it just... is or isn't. iconic behaviour.
• d,derived — optional ✨ switch: which haplotype to count, "00" vs "11". the default is "00". (the original even leaves a lil trailing comma on this line, and honestly? she ate. 🙈)

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Type: transformation 🦋

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✨ EXIT VALUES ✨

she keeps it simple, and honestly we love that for her:

• 0 — Success 🎉 slay, you did it, the LD got computed.
• not 0 — Failure 💀 something went wrong, go check your flags, bestie, I believe in you.

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✨ SEE ALSO ✨

• vcflib(1) — go say hi to the family, she doesn't exist in a vacuum. 🌈

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✨ OTHER ✨

💖 LICENSE 💖

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

MIT licensed means it's free, it's open, it's generous, we stan. 👑

💖 AUTHORS 💖

Erik Garrison and vcflib contributors. 🫶 absolute legends, every single one of them.

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and that's the whole page, bestie!! 🌸 this was vcfld (vcflib) — the version/source tag from the footer, and yeah, the header up top said vcfld (VCF transformation), so now you have both, you're welcome. go compute some LD, drink some water, and remember: zero base lists start at 0. mwah. 💅✨🎀🦋💜