VCF-COMPARE(1)

📦 version 0.1.17, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💅 VCF-COMPARE — bestie edition

okay so this is vcf-compare, a User Command, and it's about to be your new fave. no cap. 🦋

✨ NAME ✨

vcf-compare — compare bgzipped and tabix indexed VCF files 🧬

🌸 SYNOPSIS 🌸

compare-vcf [OPTIONS] file1.vcf file2.vcf ...

💖 DESCRIPTION 💖

About: compare bgzipped and tabix indexed VCF files. periodt.

like, the whole vibe is: you got your VCF files all compressed and indexed, and now you wanna see how they stack up against each other. the way to prep them is literally this:

bgzip file.vcf; tabix -p vcf file.vcf.gz

that's it, that's the ritual. do that and you're main character ready. 👑

🎀 OPTIONS 🎀

  • -c, --chromosomes <list|file> — literally the same thing as -r, it's just hanging around for backward compatibility. please do not use it tho, because it's getting dropped in the future. it's giving deprecated. 💀
  • -d, --debug — debugging info! and the more times you pass it, the more it yaps. give it once, give it twice, it just gets chattier. 🔥
  • -H, --cmp-haplotypes — compare the actual haplotypes, not just the positions. like, get into the details bestie. 💅
  • -m, --name-mapping <list|file> — use this with -H when your files have different column names (awkward 😭). the argument is either a comma-separated list or one mapping per line in a file. the names are colon separated and must appear in the same order as the files on the command line. no shuffling. 🙈
  • -R, --refseq <file> — compare the actual sequence, not just positions. pair it with -w if you wanna compare indels. iconic combo. ✨
  • -r, --regions <list|file> — process the given regions (comma-separated list, or one region per line in a file). 🗺️
  • -s, --samples <list> — process only the listed samples. and ngl, dropping the samples you don't care about can speed things up considerably. performance slay. ⚡
  • -w, --win <int> — in repetitive sequences, the same indel can get called at different positions (rude). so this says: consider records this far apart as matching — be it a SNP or an indel. 🫶
  • -h, -?, --help — this help message. hi bestie 👋
fr fr, keep that -c out of your scripts. she's on her way out. 🚪

vcf-compare 0.1.5, from July 2011 — yeah she's an elder but she still eats. mwah, love u, go compare some VCFs. 💜🌈

📦 where this page comes from