HAPLRT(1)

✨ HAPLRT(1) ✨

okay bestie, welcome to hapLrt — the hapLrt (VCF genotype) girlies' manual page 💖

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🌸 NAME 🌸

hapLrt — literally the whole name, that's it, that's the icon 👑

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🎀 SYNOPSIS 🎀

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

that's the vibe check, run it and slay 💅

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🦋 DESCRIPTION 🦋

HapLRT is a likelihood ratio test for haplotype lengths. no cap. 🧬

The lengths are modeled with an exponential distribution. periodt.

The sign denotes if the target has longer haplotypes (1) or the background (-1). it's giving directional, fr fr ⭐

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✨ OPTIONS ✨

okay so first, the tea on the Output : 4 columns : 🫖 (yes she said 4, but look at the list, bestie — we report what she says, always 🙈)

1. seqid
2. position
3. mean target haplotype length
4. mean background haplotype length
5. p-value from LRT
6. sign

• t, target — required! argument: a zero base comma separated list of target individuals corresponding to VCF columns 💖
• b, background — required! argument: a zero base comma separated list of background individuals corresponding to VCF columns 🦋
• f, file — required! argument: a properly formatted phased VCF file 📁
• y, type — required! argument: type of genotype likelihood: PL, GL, GT or GP 🌈
• r, region — optional, lowkey the fun one ✨ argument: a genomic range to calculate hapLrt on in the format : "seqid:start-end" or "seqid" 🗺️

Type: genotype 🧬

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💀 EXIT VALUES 💀

• 0 — Success 👑 (we ate)
• not 0 — Failure 😭 (we did not eat)

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🔥 SEE ALSO 🔥

• vcflib(1) — go read the family lore, 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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ngl bestie, -t and -b and -f and -y are required, so don't come to the function without them, the LRT will simply not run and that's embarrassing 🙈

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and that's the page!! hapLrt (vcflib) — this whole manual page lives under hapLrt (vcflib), and it's dated right along with it, so that's the source, version and date energy, signed off with love 🎀✨ bye bestie, go run it 💖