GENOTYPESUMMARY(1)

💖 GENOTYPESUMMARY(1) 💖

okay bestie, welcome to genotypeSummary — it's the VCF statistics girlie from the vcflib crew, and she's here to count genotypes for you. no cap.

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✨ NAME ✨

genotypeSummary — she summarizes, she counts, she serves 💅

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🌸 SYNOPSIS 🌸

genotypeSummmary –type PL –target 0,1,2,3,4,5,6,7 –file my.vcf –snp

(and yes, the three m's in genotypeSummmary up there are exactly what the original says — we do not edit the ancestors 🙈)

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🦋 DESCRIPTION 🦋

She generates a table of genotype counts. That's the whole vibe. Summarizes genotype counts for bi-allelic SNVs and indel. like, that's her job, that's her moment, she ate. 👑

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🎀 OPTIONS 🎀

• output — table of genotype counts for each individual. that's the tea you're getting back 🍓
• required: t,target — a zero based comma separated list of target individuals corresponding to VCF columns
• required: f,file — proper formatted VCF
• required, y,type — genotype likelihood format; genotype : GL,PL,GP
• optional, r,region — a tabix compliant region : chr1:1-1000 or chr1
• optional, s,snp — Only count SNPs
• optional, a,ancestral — describe counts relative to the ancestral allele defined as AA in INFO
• Type: statistics

bestie the t,target, f,file and y,type ones are required — do not skip them, she will simply not run, periodt. 💀

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⭐ EXIT VALUES ⭐

• 0 — Success ✨ (the good ending)
• not 0 — Failure 😭 (the other ending)

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🌈 SEE ALSO 🌈

• vcflib(1)

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💜 OTHER 💜

nothing to see here, just vibes 🧚

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🔥 LICENSE 🔥

Copyright 2011-2024 (C) Erik Garrison and vcflib contributors. MIT licensed. Copyright 2020-2024 (C) Pjotr Prins.

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👑 AUTHORS 👑

Erik Garrison and vcflib contributors.

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okay that's the whole page, you're basically a genotypeSummary expert now, iykyk 🫶 this lil manual page came to you straight from genotypeSummary (vcflib) — go forth and count some genotypes, bestie 💖✨🌸