VCFANNO(1)

📦 version 0.3.7, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

🌸 VCFANNO 💖

okay bestie, so this is the manual for vcfanno — section 1 of the manuals, filed under User Commands, and yeah, she's a whole vibe. Let's get into it 🫶

✨ NAME ✨

vcfanno — annotate a VCF with other VCFs/BEDs/tabixed files

like. that's the whole job. she takes your VCF and sprinkles other files' info all over it. iconic behavior fr fr 💅

🌈 DESCRIPTION 🌈

first up, the little banner she prints at you when you run her. it's giving ✨opening credits✨:

============================================= vcfanno version 0.3.2
[built with go1.14.4]

see: https://github.com/brentp/vcfanno
============================================= Usage of vcfanno:
📌 note the deets: vcfanno version 0.3.2, and she was built with go1.14.4. and yes, that github link is right there — https://github.com/brentp/vcfanno — go look, she's cute. 🦋

🎀 Usage of vcfanno 🎀

here's every single flag, no cap, nothing skipped, because we do NOT gatekeep in this house 👑

  • -base-path string — an optional base-path that gets prepended to your annotation files in the config. basically "hey bestie, all my files live over here, save me some typing" 💖
  • -ends — annotate the start and the end as well as the interval itself. not just the middle, the whole lil sandwich 🥪✨
  • -lua string — optional path to a file containing custom javascript functions to be used as ops. (yes, it's called -lua and it says javascript, i don't make the rules, i just report them 💀)
  • -p int — number of processes to use. default is 2. parallelize, girlboss, get that throughput 🌸
  • -permissive-overlap — annotate with an overlapping variant even if it doesn't share the same ref and alt alleles. default behavior is to require an exact match between variants. so without this flag she's picky, with it she's chill. lowkey the whole personality switch 🔥

👑 AUTHOR 👑

this manpage was written by Nilesh Patra for the Debian distribution, and can be used for any other usage of the program. ty for your service, we appreciate you 🫶💜

and that's the whole page bestie, mwah 💅 — this was vcfanno 0.3.2+ds, dated July 2020, and it lives in the VCFANNO(1) section of the manual. go annotate something, you got this 🌟🎀🦋

📦 where this page comes from