VCFFIXUP(1)

💖 VCFFIXUP 💖

okay bestie, so you know that manual page vcffixup(1) from the vcflib crew? yeah. we're doing that one. it's a VCF transformation tool and it's lowkey iconic, let's get into it 🦋

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✨ NAME ✨

vcffixup — that's the whole name, short and sweet, main character energy fr fr 💅

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🌸 SYNOPSIS 🌸

vcffixup

that's it. that's the whole vibe. no flags, no drama. she just runs. 👑

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🎀 DESCRIPTION 🎀

okay so here's the tea: vcffixup generates a VCF stream where AC and NS have been generated for each record, using the sample genotypes. no cap. it literally looks at the genotypes in your records and produces those fields for you.

like, it's giving "let me fix your annotation for you bestie" 🫶

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💖 OPTIONS 💖

okay so there's exactly one blob of option text here and it's doing a lot, so let's break it down:

• the allele-frequency behavior — count the allele frequencies across alleles present in each record in the VCF file. (Similar to vcftools --freq.) 📊
• the genotype-correction behavior — uses genotypes from the VCF file to correct AC (alternate allele count), AF (alternate allele frequency), NS (number of called), in the VCF records. literally fixing them up. hence the name, iykyk 😌

for example:

% vcfkeepsamples file.vcf NA12878 | **vcffixup** - | vcffilter -f "AC > 0"

would downsample file.vcf to only NA12878, removing sites for which the sample was not called as polymorphic. periodt. 💜

• Type — transformation ✨

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🦋 EXIT VALUES 🦋

• 0 — Success 🎉 (she ate, no crumbs)
• not 0 — Failure 😭 (it's giving tragedy, check your inputs)

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🌈 SEE ALSO 🌈

• vcflib(1) — go read the parent page bestie, it's the whole fam 🧚

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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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just a heads up bestie — this one is a transformation type, so it's meant to sit in a pipe and do its little glow-up on the stream as it goes by. 🍓

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and that's the whole page, no notes. this was vcffixup from the vcflib collection — mwah, go forth and annotate responsibly, ily 💖✨🎀