VCF-ISEC(1)

💖 VCF-ISEC(1) 💖

okay bestie, buckle up, because this is vcf-isec, a User Command (section 1 of the manual, we love a classic), and it's genuinely iconic. it makes intersections, unions, complements on bgzipped and tabix indexed VCF or tab-delimited files. yes. all of that. slay.

✨ NAME ✨

vcf-isec — create intersections, unions, complements on bgzipped and tabix indexed VCF or tab-delimited files 🦋

🌸 SYNOPSIS 🌸

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

👑 DESCRIPTION 👑

About: Create intersections, unions, complements on bgzipped and tabix indexed VCF or tab-delimited files. that's the whole vibe, that's the assignment, and it ate. 💅

⚠️ heads up bestie: note that lines from all files can be intermixed together on the output, which can yield unexpected results. not me finding out the hard way 😭

💜 OPTIONS 💜

• -C, --chromosomes <list|file> — process the given chromosomes. you can hand it a comma-separated list, or a file with one chromosome per line. either way, we're being picky and i respect it. ✨
• -c, --complement — output positions present in the first file but missing from the other files. the "everyone else ghosted" list. 👻
• -d, --debug — debugging information. for when you need to see the receipts. 🔍
• -f, --force — continue even if the script complains about differing columns. it's giving "i know she's messy but i love her". 🙈
• -o, --one-file-only — print only entries from the left-most file. without -o, all unique positions will be printed. main character file only, no ensemble cast. 👑
• -n, --nfiles [+-=]<int> — output positions present in this many files. the sign is the whole point, bestie:
  • = → exactly this many
  • + → this many or more
  • - → this many or fewer
• -p, --prefix <path> — if present, multiple files will be created with all possible isec combinations. (suitable for Venn Diagram analysis.) it's giving arts and crafts but make it genomics 🎀
• -t, --tab <chr:pos:file> — tab-delimited file with indexes of chromosome and position columns. (1-based indexes, so don't come at it with your 0-based nonsense)
• -w, --win <int> — in repetitive sequences, the same indel can be called at different positions. consider records this far apart as matching (be it a SNP or an indel). so basically, close enough counts. 🫶
• -h, -?, --help — this help message. hi, hello, welcome, here's everything. 💖

🌈 EXAMPLES 🌈

bgzip file.vcf; tabix -p vcf file.vcf.gz bgzip file.tab; tabix -s 1 -b 2 -e 2 file.tab.gz

and that's the page, bestie!! go forth and intersect. periodt. 🧚💅

this was vcf-isec version 0.1.5, from July 2011 — yes she's vintage, yes she still serves. mwah. 💋