CYVCF2(1)

📦
version 0.32.0 · 7 versions
, in ubuntu stonking

💖 CYVCF2 💖

okay bestie, sit down, hydrate, and let me tell you about cyvcf2 — it's a little command-line icon from the User Commands section of the manual (section 1, iykyk), and it is fast parsing of VCF and BCF including region-queries. that's literally the whole vibe. no cap.

✨ NAME ✨

cyvcf2 — fast parsing of VCF and BCF including region-queries 🧬💅

🦋 SYNOPSIS 🦋

cyvcf2 [OPTIONS] <vcf_file> or -

so you feed it a <vcf_file>, OR you hit it with a - and it'll read from stdin like the flexible queen she is. the <vcf_file> and the - are alternatives, not a snack combo. 🍓

🌸 DESCRIPTION 🌸

fast vcf parsing with cython + htslib 🌈⚡

that's it. that's the description. she's fast, she's cython-and-htslib-powered, and she is not here to waste your time. periodt.

👑 OPTIONS 👑

every single one, bestie, we're not skipping a crumb:

  • -c, --chrom TEXT — Specify what chromosome to include. 🧬 give her a chromosome and she'll keep it.
  • -s, --start INTEGER — Specify the start of region. takes an INTEGER, so not a vibe, a number.
  • -e, --end INTEGER — Specify the end of the region. also an INTEGER. yes, -s and -e are giving region-query main character energy. 🔥
  • --include TEXT — Specify what info field to include. you tell her which info field you want in, and she keeps it.
  • --exclude TEXT — Specify what info field to exclude. opposite energy: you name it, she drops it. 💀
  • -i, --individual TEXT — Only print genotype call for individual. one (1) individual, one (1) genotype call, no extras. 🙈
  • --no-inds — Do not print genotypes. genotypes? not today. not on her watch.
  • --loglevel [DEBUG|INFO|WARNING|ERROR|CRITICAL] — Set the level of log output. <pink>[default: INFO]</pink> — so the choices are DEBUG, INFO, WARNING, ERROR, or CRITICAL, and if you don't say anything she's just gonna INFO quietly to herself. pick DEBUG if you want her to tell you EVERYTHING. 🗣️
  • --silent — Skip printing of vcf. she does the work, she just doesn't tell anyone. lowkey mysterious. 🫶
  • --help — Show this message and exit. the classic. the moment of need. use it, bestie, it's free. ⭐
heads up bestie: --help is the one that bounces out after showing you the message, and --silent is the one that keeps the vcf off your screen entirely. don't get it twisted. 💖

🎀 a little sign-off 🎀

this whole manual page is cyvcf2 0.32.0, dated February 2026, and it lives in the CYVCF2(1) corner of the manual. she's iconic, she's fast, and she's parsing VCF and BCF for you. slay. 💅✨🦋

📦 where this page comes from