VCFINTERSECT(1)

👑 VCFINTERSECT(1) — the vcfintersect page, but make it cute

okay bestie, sit down, hydrate, and let me tell you about vcfintersect — part of the vcflib fam, filed under VCF transformation. she does VCF set analysis and honestly? she ate. 💅

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✨ NAME ✨

vcfintersect — that's her, that's the name, no notes.

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🌸 SYNOPSIS 🌸

vcfintersect options []

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🦋 DESCRIPTION 🦋

VCF set analysis. that's the whole vibe. she looks at your VCF and she does set math on it, fr fr. 🧚

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💖 OPTIONS 💖

here's the full roster, no skips, no cuts, every single one of them, periodt:

• -b, --bed FILE — use the intervals that this BED file hands you.
• -R, --region REGION — use a 1-based tabix-style region (like chrZ:10-20 for example). you can pass multiples, she's flexible like that.
• -S, --start-only — don't use the reference length info in the record to figure out overlap status; just go off the start position. simple. minimal. iconic.
• -v, --invert — invert the selection, so you only print the records that would not have been printed out. the opposite girlie. 🔄
• -i, --intersect-vcf FILE — use this VCF for set intersection generation.
• -u, --union-vcf FILE — use this VCF for set union generation.
• -w, --window-size N — compare records that are up to this many bp away (default 30).
• -r, --reference FILE — FASTA reference file. required if you're using -i and -u, don't forget it bestie. 🫶
• -l, --loci — output whole loci when one alternate allele matches.
• -m, --ref-match — intersect based on the record's REF string.
• -t, --tag TAG — stick TAG onto each record's info field if it would intersect.
• -V, --tag-value VAL — use this value to say the allele is passing. anything else gets '.' instead. default: 'PASS'.
• -M, --merge-from FROM-TAG
• -T, --merge-to TO-TAG — merge from FROM-TAG used in the -i file, setting TO-TAG in the current file.

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🎀 the tea on bed-vcf intersection

for bed-vcf intersection, alleles that fall into the targets are retained. that's it, that's the rule. 💜

🌈 haplotype aware intersection, union and complement

haplotype aware intersection, union and complement. use this for intersection and union of VCF files: she unifies on equivalent alleles within window-size bp, as determined by haplotype comparison alleles. ✨

also she's a transformation type. just so you know. 👑

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💀 EXIT VALUES 💀

• 0 — Success. slay. 🎉
• not 0 — Failure. it's giving tragic. 😭

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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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and that's the page!! this one lives under vcfintersect (vcflib) — mwah, go intersect something responsibly, ily, byeee 💖✨🎀🦋