VT(1)

📦 version 0.57721, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

✨ NAME ✨

vt — the toolset for short variant discovery in genetic sequence data 🧬💖

okay so bestie, this is a User Commands page, which is just fancy talk for "a program you run in your terminal," and vt is here to be your little genetics bestie. no cap. 🫶

🌸 SYNOPSIS 🌸

vt <tool> [options]

like… that's it. you pick a tool (there are SO many, keep reading 💅) and then you hand it whatever [options] it wants. it's giving "choose your own adventure" but for genomes. 🌈

👑 TOOLS 👑

bestie. sit down. here's the whole roster, and yes, every single one of them is iconic in its own way. ✨

  • view — view vcf/vcf.gz/bcf files. literally just look at them. no notes. 👀
  • index — index vcf.gz/bcf files, so everything else can find stuff fast. the backstage crew of this whole operation fr fr. 🎀
  • normalize — normalize variants. yes, like a skincare routine but for variants. 💅
  • decompose — decompose variants. breaking them down, main character style. 💀
  • uniq — drop duplicate variants. we do NOT do repeats here. 🚫
  • cat — concatenate VCF files. smash them together, bestie. 🫂
  • paste — paste VCF files. (yes, cat and paste both exist, and yes, they are different, don't @ me.) 🙈
  • sort — sort VCF files. everything in its rightful place, periodt. 👑
  • subset — subset VCF file to variants polymorphic in a sample. tiny little curated collection, very aesthetic. 🎀
  • peek — summary of variants in the vcf file. a little sneak peek, hence the name, she's clever like that. ✨
  • partition — partition variants. dividing them up, fair and square. 🌸
  • multi_partition — partition variants from multiple VCF files. the partition girlie but she brought friends. 🔥
  • annotate_variants — annotate variants. notes in the margins, but make it science. 📝
  • annotate_db_rsid — annotate variants with dbSNP rsid. 🏷️
  • annotate_1000g — annotate variants with 1000 Genomes variants. 🌍
  • annotate_regions — annotate regions. 🗺️
  • compute_concordance — compute genotype concordance between 2 call sets. comparing, like a vibe check but with numbers. 💯
  • compute_features — compute genotype likelihood based statistics. math girlies rise. 🧮
  • discover — discover variants. go find them, queen. 🔍
  • genotype — genotype variants. the final boss of the list, and she ate. 👑

🦋 SEE ALSO 🦋

Help page on http://statgen.sph.umich.edu/wiki/Vt — go read it, it's right there, iykyk. 📖💜

💖 AUTHOR 💖

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. 🫶 (ty Andreas, king behaviour.)

and that's the whole page bestie!! this was vt version 0.57721+ds, dated June 2020, and she's still serving. mwah. 💅✨🎀

📦 where this page comes from