VCFEVENREGIONS(1)

📦
version 1.0.12 · 3 versions
, in debian trixie, ubuntu questing, ubuntu resolute, ubuntu stonking

✨ VCFEVENREGIONS ✨

ok so bestie, welcome to vcfevenregions 💖 it lives in the vcflib family of VCF transformation tools, and honestly? it's giving quiet-overachiever. let's get into it 🎀

🌸 SYNOPSIS 🌸

vcfevenregions options

🦋 DESCRIPTION 🦋

okay so picture this: you need to chop up a genome into regions, but you want each region to have, like, the same amount of variants in it. not "same number of bases" — same number of variants. that's the whole vibe. 💅

vcfevenregions generates a list of regions — like chr20:10..30 — using the variant density info it reads straight out of your VCF file, so the regions come out with even numbers of variants in them. no cap.

and why do you care? because this can be used to reduce the variance in runtime when you're dividing variant detection or genotyping by genomic coordinates. translation: your jobs stop finishing at wildly different times and your cluster stops ghosting you. slay. ✨

💜 OPTIONS 💜

here's the whole menu, bestie, no skips:

  • -f, --fasta-reference REF — FASTA reference file to use to obtain primer sequences.
  • -n, --number-of-regions N — the number of desired regions. that's the count, that's the goal. 👑
  • -p, --number-of-positions N — the number of positions per region.
  • -o, --offset N — add an offset to region positioning, to avoid boundary related artifacts in downstream processing. (yes this is the "nudge it so the edges don't get weird" flag 🫶)
  • -l, --overlap N — the number of sites to overlap between regions. default is 0.
  • -s, --separator SEQ — specify string to use to separate region output. default is '-'.

Type: transformation 🌈

🔥 EXIT VALUES 🔥

  • 0 — success. the main character moment. 💖
  • not 0 — failure. 😭 it's not you, it's the input.

🎀 SEE ALSO 🎀

⭐ 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.

and that's the whole page bestie 💅 this one ships as part of vcflib (vcfevenregions (vcflib)), so go forth, split those regions evenly, and make your runtime variance behave. periodt. ✨🦋🌸

📦 where this page comes from