VCFFLATTEN(1)

💖 vcfflatten — the manual page, bestie edition 💖

ok so you're reading the vcfflatten(1) page from the vcflatten (VCF transformation) manual and honestly? you came to the right place. this lil tool is iconic, let's get into it.

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✨ NAME ✨

vcfflatten — that's it, that's the name, no cap 💅

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🌸 SYNOPSIS 🌸

vcfflatten [options][file] -h –help display this help message and exit.
-i –ignore-errors do not flatten locus if `AF' is not specified.

not me showing you the synopsis exactly as written, including the em-dashes, because we do NOT edit the sacred text 🙈

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🦋 DESCRIPTION 🦋

ok so here's the vibe: vcfflatten removes multi-allelic sites by picking the most common alternate. periodt.

but — and this is the important part — it requires allele frequency specification AF, and it needs you to use G and A to specify the fields which vary according to the Allele or Genotype. like, that's not optional, that's the whole thing. no AF, no flatten. 💀

your VCF file can be specified on the command line, or you can pipe it in as stdin. main character energy either way 🫶

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✨ OPTIONS ✨

Type: transformation ✨

• -h, –help — display this help message and exit. the "hey bestie what is this" button 🎀
• -i, –ignore-errors — do not flatten locus if AF is not specified. it's giving "we're not doing anything weird here, we're just skipping it" 🙈

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💜 EXIT VALUES 💜

• 0 — Success 🎉 slay, it worked
• not 0 — Failure 😭 something went wrong, cry about it (then read the output)

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🌈 SEE ALSO 🌈

• vcflib(1) — the whole family, iykyk

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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 was vcfflatten (vcflib) — vcflib's very own, written by Erik Garrison and the vcflib contributors, MIT licensed, © 2011-2024 and © 2020-2024 Pjotr Prins. now go flatten some loci, you've got this 🧚✨