MELTEHH(1)

💖 MELTEHH(1) — meltEHH, the VCF statistics girlie 💖

okay so bestie, welcome to meltEHH from the vcflib family 🧚 this is the manual page, and I'm gonna walk you through every single bit of it, no skips, no shortcuts, periodt ✨

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🌸 SYNOPSIS 🌸

meltEHH –target 0,1,2,3,4,5,6,7 –pos 10 –file my.phased.vcf  –region chr1:1-1000 > STDOUT 2> STDERR

that's the whole vibe, literally just that 🫶

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🦋 DESCRIPTION 🦋

meltEHH hands you the data you need to plot extended haplotype homozygosity (EHH) curves, and it also produces the data to generate this iconic little plot right here:

<img src="https://github.com/vcflib/vcflib/blob/master/examples/example-ehh.png?raw=true" alt="" width=400>

like. it's giving data-viz main character energy 💅

meltEHH provides the data to plot EHH curves.

Output : 4 columns :

1. seqid
2. position
3. EHH
4. ref or alt [0 == ref]

four columns, that's it, that's the whole serve 🎀

Params:

• required: t,target <STRING> — a zero base comma separated list of target individuals corresponding to VCF columns 🌈
• required: r,region <STRING> — a tabix compliant genomic range, format: "seqid:start-end" or "seqid" 🗺️
• required: f,file <STRING> — proper formatted and phased VCF. yes bestie, phased, we're not playing 🙈
• required: y,type <STRING> — genotype likelihood format: GT, PL, GL, GP ⭐
• required: p,position <INT> — variant position to melt 🫠
• optional: a,af <DOUBLE> — alternative alleles with frequencies less than [0.05] are skipped 💀

Type: statistics

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✨ OPTIONS ✨

(okay so the options are all chillin' up in the Params list above — that's where the whole flag family lives 💜)

• -t, --target <STRING> — required. zero base comma separated list of target individuals corresponding to VCF columns 👑
• -r, --region <STRING> — required. a tabix compliant genomic range, format: "seqid:start-end" or "seqid" 🌸
• -f, --file <STRING> — required. proper formatted and phased VCF 📁
• -y, --type <STRING> — required. genotype likelihood format: GT, PL, GL, GP 🧬
• -p, --position <INT> — required. variant position to melt 🔥
• -a, --af <DOUBLE> — optional. alternative alleles with frequencies less than [0.05] are skipped 🍓

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💀 EXIT VALUES 💀

• 0 — Success 🎉 slay, it worked
• not 0 — Failure 😭 something went sideways 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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meltEHH (vcflib) — and that's the whole page bestie, ty for coming to my TED talk, ily, go melt some haplotypes 💖✨🦋🌸💅🫶👑🌈⭐🍓🧚💜