SEQUENCEDIVERSITY(1)

💖 NAME 💖

okay so bestie, this is sequenceDiversity — yes, the manual name is literally just that, no extra crumbs. it's giving lowercase-camelCase icon behaviour and we're obsessed. ✨

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🌸 SYNOPSIS 🌸

sequenceDiversity –target 0,1,2,3,4,5,6,7 –file my.vcf

that's it. that's the whole vibe. you point it at some targets and a VCF and it goes to work 💅

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🦋 DESCRIPTION 🦋

so sequenceDiversity is the program that calculates two of the most popular metrics for haplotype diversity, and no we're not gatekeeping them: they're pi and extended haplotype homozygosity (aka eHH). 🔥

Pi gets computed using the Nei and Li 1979 formulation — that's the receipts, periodt.

eHH is honestly just a really convenient way to think about haplotype diversity, like a little vibe check for your window:

• when eHH = 0, every haplotype in the window is unique — all main characters, no copies 🌈
• when eHH = 1, every haplotype in the window is identical — matching outfits, head to toe 👑

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✨ OPTIONS ✨

📊 Output : 5 columns

okay so when it prints, it's printing 5 columns, in this exact order, no notes:

1. seqid
2. start of window
3. end of window
4. pi
5. eHH

🎀 the actual flags

• t, target — required 🫶 argument: a zero base comma separated list of target individuals corresponding to VCF columns
• f, file — required 💖 argument: a properly formatted phased VCF file
• y, type — required ⭐ argument: type of genotype likelihood, so one of PL, GL or GP
• a, af — optional 🌸 sites less than af are filtered out; default is 0
• r, region — optional 🧚 argument: a tabix compliant region, so either "seqid:0-100" or just "seqid"
• w, window — optional 💜 argument: the number of SNPs per window; default is 20

Type: statistics — that's the category tag, iykyk 📌

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💀 EXIT VALUES 💀

• 0 — Success ✨ slay, it worked, we love that for you
• not 0 — Failure 😭 something went sideways, go check your inputs bestie

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🌈 SEE ALSO 🌈

• vcflib(1)

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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 — brought to you by sequenceDiversity from the vcflib family, catalogued under sequenceDiversity (VCF statistics), and yes the footer literally just says sequenceDiversity (vcflib) because it knows its own name and needs no date to be iconic. periodt. 💖✨🎀