VCFGENOTYPES(1)

💖 vcfgenotypes 💖

okay so bestie, welcome to vcfgenotypes, a lil member of the vcflib crew (that's the manual section 1 squad, iykyk). she's a tiny program with main character energy and one job: making your genotypes make sense to actual humans. ✨

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🌸 SYNOPSIS 🌸

vcfgenotypes

that's it. no flags, no args, no drama. she's serving minimalism 💅

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🦋 DESCRIPTION 🦋

so here's the vibe: vcfgenotypes reports the genotypes for each sample, for each variant in the VCF. that's it, that's the whole gig.

and the part that's actually iconic? it converts the numerical representation of genotypes that the GT field hands you (all those cryptic little digits, we've all been there 😭) into a human-readable genotype format. so instead of squinting at numbers like it's a pop quiz, you get actual allele letters. slay. 👑

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✨ OPTIONS ✨

...yeah bestie, there are none 🙈 no options, no flags, nothing to configure. she takes no arguments and needs no convincing. periodt.

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🎀 EXAMPLES 🎀

here's the example, and ngl it's kind of beautiful:

**vcfgenotypes** samples/sample.vcf

and the output?? look at her:

19      111     A       C       A,C     NA00001:A/A     NA00002:A/A     NA00003:A/C
19      112     A       G       A,G     NA00001:A/A     NA00002:A/A     NA00003:A/G
20      14370   G       A       G,A     NA00001:G/G     NA00002:G/A     NA00003:A/A
20      17330   T       A       T,A     NA00001:T/T     NA00002:T/A     NA00003:T/T
20      1110696 A       G,T     A,G,T   NA00001:G/T     NA00002:G/T     NA00003:T/T
20      1230237 T       .       T,.     NA00001:T/T     NA00002:T/T     NA00003:T/T
20      1234567 G       GA,GAC  G,GA,GAC        NA00001:G/GA    NA00002:G/GAC   NA00003:GA/GA
20      1235237 T       .       T,.     NA00001:T/T     NA00002:T/T     NA00003:./.
X       10      AC      A,ATG   AC,A,ATG        NA00001:AC      NA00002:AC/A    NA00003:AC/ATG

like, the ./. on that one row?? we've all had days like that fr. 🫶

Type: statistics

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🔥 EXIT VALUES 🔥

• 0 — Success 💖 everything went great, she ate
• not 0 — Failure 💀 something went sideways, no cap

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🌈 SEE ALSO 🌈

• vcflib(1) — the whole family, go say hi

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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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okay that's the whole page bestie, go forth and decode some genotypes 🌸

this has been vcfgenotypes from the vcflib manual, page VCFGENOTYPES(1) — catch you in the next one, mwah 💅💖