ABBA-BABA(1)

🎀 ABBA-BABA(1) 🎀

ABBA-BABA(1) is the manual page for abba-baba, so let's get into it 💖

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✨ NAME ✨

abba-baba 🦋 That's the whole name. Short and iconic.

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🌸 SYNOPSIS 🌸

abba-baba –tree 0,1,2,3 –file my.vcf –type PL

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💅 DESCRIPTION 💅

Okay bestie, so abba-baba figures out the tree pattern for four individuals ✨ It's giving precision. It assumes the reference is ancestral and skips any sites that aren't abba-baba sites, so it's not wasting time on the rest 💀

The output is a boolean value: 1 means true and 0 means false, for both abba and baba. Also, the tree argument should be listed from the most basal taxa to the most derived, so oldest to newest. No cap, the order matters 🌈

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🔥 OPTIONS 🔥

Here's the vibe check for the tree shape 👑

    Example:
    D   C  B   A
    \ /  /    /
     \  /    /
      \    /
       \  /
        /
       /
--tree A,B,C,D

The output is 4 columns 🍓

1. seqid
2. position
3. abba
4. baba

Now the options. All three are required 🫶

• -t, --tree — required 💖 A zero-based, comma-separated list of target individuals that lines up with the VCF columns.
• -f, --file — required 📁 A properly formatted VCF.
• -y, --type — required 🧚 The genotype likelihood format. Pick from GP, GL or PL.

Type: genotype ✨

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🦋 EXIT VALUES 🦋

• 0 — Success, you did it bestie 🎉
• not 0 — Failure 😭

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🌈 SEE ALSO 🌈

• vcflib(1) 💜 Go check it out, it's the whole family.

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🫧 OTHER 🫧

Nothing in here, bestie 🙈

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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. The icons 🫶

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Okay that's the whole tea ☕ Source is abba-baba (vcflib) and the manual is ABBA-BABA(1). Now go be iconic 💖🦋✨