VCF-SUBSET(1)

💖 vcf-subset — create subset of VCF file 💖

okay bestie, so vcf-subset is a lil command from the User Commands corner of the manual, and it does exactly what it says on the tin: it makes you a subset of a VCF file. slay. ✨

🌈 SYNOPSIS 🌈

vcf-subset [OPTIONS] in.vcf.gz > out.vcf

like… you feed it a vcf, you get a smaller vcf out the other side. the > redirect is doing the heavy lifting there, bestie, don't forget it. 💅

✨ OPTIONS ✨

• -c, --columns <string> — a file or a comma-separated list of the columns you wanna keep in the vcf file. if you hand it a file, it's one column per row. your choice, queen. 👑
• -e, --exclude-ref — excludes the rows that don't contain variants. bye-bye reference-only rows, you will not be missed. 🙈
• -p, --private — only prints rows where only the subset columns carry an alternate allele. private? more like exclusive. 💅
• -r, --replace-with-ref — replaces the excluded types with the reference allele instead of a dot. dot says nothing, this one actually speaks up. 🎀
• -t, --type <list> — comma-separated list of the variant types to include: SNPs,indels. pick your fighters. 🔥
• -u, --keep-uncalled — do not exclude rows without calls. keep the uncalled ones, they're valid too. 🫶
• -h, -?, --help — this help message. always there for you when you're lost, fr fr. 😭

🦋 EXAMPLES 🦋

here's the vibe, in one line:

cat in.vcf | vcf-subset -r -t indels -e -c SAMPLE1 > out.vcf

cat the vcf, pipe it in, ask for indels only, swap the excluded types for reference with -r, drop the no-variant rows with -e, keep just the SAMPLE1 column with -c, and boom — out.vcf. main character energy, no cap. ⭐

lowkey reminder bestie: -c will take a file or a comma-separated list, and if it's a file it's one column per row. don't come for me when you forget. 💜

and that's the whole page, gorgeous. this one's from vcf-subset 0.1.5, dated July 2011 — vintage but still eating, periodt. 🍓🧚‍♀️💖