VCF2FASTA(1)

💖 vcf2fasta — the vcflib glow-up 💖

okay bestie, gather round, because this lil cutie vcf2fasta is out here turning your VCF into FASTA files and honestly? it's giving main character energy. it lives in vcflib (that's section 1 of the manual, iykyk) and it's a transformation-type tool, which is exactly what it sounds like: it transforms stuff. slay.

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✨ SYNOPSIS ✨

vcf2fasta options [file]

that's it. that's the whole vibe. you give it options, you maybe give it a file, it does the thing. periodt.

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🦋 DESCRIPTION 🦋

okay so here's what's actually happening under the hood, and it's lowkey iconic:

it generates sample_seq:N.fa for each sample, each reference sequence, and each chromosomal copy N in [0,1... ploidy]. yes, every combo. she's thorough like that. 💅

and the naming? each sequence inside the fasta file is named using the same pattern used for the file name, which means you can literally just combine them all together later. no cap. that's the whole point — everything lines up, everything matches, and your downstream self will thank you. 🫶

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💅 OPTIONS 💅

okay here's the options list, and no I'm not skipping any of them, we're doing all of them because that's what besties do:

• -f, --reference REF — use this reference when decomposing samples. hand her the REF and she'll decompose against it. iconic behavior.
• -p, --prefix PREFIX — affix this output prefix to each file. there's none by default, so if you want a prefix you gotta ask for it, she's not gonna assume. 🙈
• -P, --default-ploidy N — sets a default ploidy for samples that don't have any information in the first record. the default here is 2. so yeah, if a sample shows up with no ploidy tea to spill, she just assumes 2. 🍓
• -n VAL — set the string value to output for missing calls. missing data? you decide what she writes down. your call, bestie.

also just so we're clear: Type: transformation. that's her whole category. that's the assignment.

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🌈 EXIT VALUES 🌈

she keeps it simple, and honestly, respect:

• 0 — Success. she ate. 💖
• not 0 — Failure. 😭 something went sideways.

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🌸 SEE ALSO 🌸

• vcflib(1) — the whole fam. 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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and that's the whole page, bestie!! this one ships as part of vcflib (that's the source/version, fr fr) — go forth and convert, you absolute legend. ⭐🧚💜