VCFLEFTALIGN(1)

✨ NAME ✨

vcfleftalign — bestie, this is the tool that scooches your indels all the way to the left 💅

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🌸 SYNOPSIS 🌸

vcfleftalign options [file]

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🦋 DESCRIPTION 🦋

Okay so here's the vibe: vcfleftalign left-aligns indels and complex variants in the input. How? First a pairwise ref/alt alignment, then a heuristic, iterative left realignment process that shifts indel representations to their absolute leftmost (5') extent. Like, ALL the way over. No crumbs left behind. 🫶

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🎀 OPTIONS 🎀

This is literally the same procedure used in the internal left alignment in freebayes, and you can use it when preparing VCF files for input to freebayes to decrease positional representation differences between the input alleles and left-realigned alignments. iykyk 🔥

options:

• -r, --reference FILE — Use this reference as a basis for realignment. Give it the reference, it does the thing. ⭐
• -w, --window N — Use a window of this many bp when left aligning (150). Default's right there, no need to stress. 💖

Left-aligns variants in the specified input file or stdin. Window size is determined dynamically according to the entropy of the regions flanking the indel. These must have entropy > 1 bit/bp, or be shorter than ~5kb. Yes bestie, entropy. The science is sciencing. 🧚

Type: transformation 👑

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💀 EXIT VALUES 💀

• 0 — Success. We ate. 🍓
• not 0 — Failure. Not the vibe. 😭

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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 — this one's vcfleftalign from vcflib, mwah 💅✨