VCF2SCOARY(1)

📦 version 1.6.16, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

✨ vcf2scoary(1) ✨

okay bestie, pull up a chair 🫶 this is the vcf2scoary manual page — a User Commands situation, she's got her own section and everything 💅

🌸 NAME 🌸

vcf2scoary — takes in vcf files and creates a presence/absence matrix of mutations in the Roary/Scoary format ✨

🦋 SYNOPSIS 🦋

vcf2scoary [-h] [--out OUT] [--types TYPES] [--version] [--force]
<VCF_file>

👑 OPTIONS 👑

🎀 positional arguments:

  • <VCF_file> — The VCF file to convert to Roary/Scoary format. literally the whole reason we're here, no cap 💖

✨ optional arguments:

  • -h, --help — show this help message and exit 🫶 the classic escape hatch
  • --out OUT — The path to the output file 🍓 tell her where to put the goods
  • --types TYPES — The types of variants to include in the output.
⚠️ NOTE: This works if TYPE=XX can be found in the INFO column of the vcf file.

The special keyword ALL includes all types. This is the default setting. Common types are snp, mnp, ins, del and complex. Give as comma-separated list. Example: --types snp,ins,del

it's giving very picky-eater energy, she will ONLY take the types you name 😭

  • --version — show program's version number and exit 🌈
  • --force — Force overwriting of output file. (If it already exists) 💀 she's gonna bulldoze whatever's there, so be sure bestie

by Ola Brynildsrud (olbb@fhi.no) 🧚

💜 AUTHOR 💜

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. 👑

and that's the whole page, bestie — you ate that 🎀

vcf2scoary 1.6.16 · January 2019 — mwah, periodt 💅✨🦋

📦 where this page comes from