VCFREMAP(1)

💖 NAME 💖

okay bestie, say hi to vcfremap — that's the name, that's the whole vibe. it's a VCF transformation girlie and she's about to remap ur variants. periodt. 🦋

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✨ SYNOPSIS ✨

vcfremap options []

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🌸 DESCRIPTION 🌸

so here's the tea ☕ — for every single alternate allele, vcfremap tries to realign it against the reference, but with a lowered gap open penalty (yes, she's being generous with the gaps, it's giving main character energy).

if that realignment is actually possible? she adjusts the cigar and the reference/alternate alleles accordingly. slay. 💅

and like, the whole point is to observe how different alignment parameters — including the context-dependent ones AND the entropy-dependent ones — influence how variants get classified and interpreted. lowkey a science experiment, highkey iconic. 🔥

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🎀 OPTIONS 🎀

here's the full menu, no skips, no shortcuts, we love an exhaustive list:

• -w, --ref-window-size N — align using this many bases flanking each side of the reference allele. window seat, both sides. 🌈
• -s, --alt-window-size N — align using this many flanking bases from the reference around each alternate allele. so like, the alt's personal little entourage of context bases. ✨
• -r, --reference FILE — the FASTA reference file. required if you're using -i and -u. no reference, no service. 🙈
• -m, --match-score N — match score for the SW algorithm. when things match, they get points. good for them. 💖
• -x, --mismatch-score N — mismatch score for the SW algorithm. the penalty for not matching. oop. 💀
• -o, --gap-open-penalty N — gap open penalty for the SW algorithm. how much it costs to start a gap. think of it as the cover charge at the gap club. 🎀
• -e, --gap-extend-penalty N — gap extension penalty for the SW algorithm. the cost of keeping that gap going. 🧚
• -z, --entropy-gap-open — use entropy scaling for the gap open penalty. entropy said "let me handle this one". 🌀
• -R, --repeat-gap-extend N — penalize non-repeat-unit gaps in repeat sequence. repeat sequences get special treatment, and non-repeat-unit gaps get called out. not me being petty to gaps. 😭
• -a, --adjust-vcf TAG — supply a new cigar as TAG in the output VCF. you pick the tag name, she does the rest. 👑

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💀 EXIT VALUES 💀

• 0 — Success. we ate. 🔥
• not 0 — Failure. it's giving tragedy. 😭

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🫶 SEE ALSO 🫶

• vcflib(1)

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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 🎀 — brought to u by vcfremap (vcflib), living under the umbrella of vcfremap (VCF transformation), with all the love and none of the timestamps. go remap something iconic ✨💖🦋