BIO-VCF(1)

BIO-VCF(1) — the vibe-coded manual 💅

okay bestie, sit down, hydrate, because we're about to talk about bio-vcf — that's the manual name, it lives in the User Commands section, and it is lowkey the most iconic way to touch a VCF file. 🧬✨

🌸 NAME 🌸

bio-vcf — a domain specific language (DSL) for processing the VCF format. no cap, it's a whole DSL, it's giving compiler energy but for genomics. 🫶

✨ SYNOPSIS ✨

bio-vcf [options] filename

that's it. that's the whole summoning ritual. filename is the star of the show, <options> are her little entourage. 👑

💖 DESCRIPTION 💖

so first things first, the receipts: bio-vcf 0.9.5 (biogem Ruby 2.7.2 with pcows) by Pjotr Prins 2015-2020. icons only. 🌟

and here's a lil demo of her in her natural habitat, feeding on a VCF like the main character she is:

bio-vcf < test/data/input/somaticsniper.vcf

now the options. there are a LOT of them. do not scroll past, they're all important, periodt. 🎀

• -i, --ignore-missing — missing data? don't care, didn't ask. ignore it. 💅
• --filter cmd — evaluate a filter on every single record. every one. no skipping. 👀
• --sfilter cmd — same energy but per sample, so evaluate that filter on each sample.
• --sfilter-samples list — filter on selected samples only (like, e.g., 0,1 — yes the original literally leaves that paren hanging open, we love an unclosed parenthesis, iconic honestly 😭)
• --ifilter, --if cmd — the include filter. letting things IN. 🫶
• --ifilter-samples list — the include set — and bestie, this implicitely defines the exclude set too. that's canon, that's what it says, keep the spelling. 💀
• --efilter, --ef cmd — the exclude filter. respectfully, get out. 🙈
• --efilter-samples list — the exclude set — and this one overrides the exclude set. yes, overriding. it said what it said. 🔥
• --add-filter name — set/add the filter field to name.
• --bed bedfile — filter on BED elements, using bedfile. 🛏️
• -e, --eval cmd — evaluate that command on each record. the classic.
• --eval-once cmd — evaluate the command exactly once (usually for header info, because headers deserve their moment too). ⭐
• --seval cmd — evaluate the command on each sample. sample-by-sample, one at a time, very thorough.
• --rewrite eval — rewrite INFO. glow-up but for your INFO field. ✨
• --samples list — output the selected samples only.
• --rdf — generate Turtle RDF 🐢 (and also check out --template! — the original says it with the bang, so the bang stays, iykyk)
• --num-threads [num] — multi-core version (default ALL). all the threads, all at once, she's got range. 🔥
• --thread-lines num — fork a thread on num lines (default 40000).
• --skip-header — do not output the VCF header info. gone. bye. 🫥
• --set-header list — set a special tab delimited output header (and #samples expands to the sample names, cute right?)
• -t, --template erb — use an ERB template for output. 🎀
• --add-header-tag — add the bio-vcf status tag to the header output. branding. 💅
• --timeout [num] — timeout waiting for a thread to complete (default 180). patience is a virtue but it does expire. ⏰
• --names — output the sample names.
• --statistics — output statistics. numbers girlies rise. 📊
• -q, --quiet — run quietly 🤫
• -v, --verbose — run verbosely 🗣️
• --debug — show debug messages and keep intermediate output. messy but honest.
• --id name — identifier.
• --tags list — add tags. 🏷️
• -h, --help — display this help and exit. the escape hatch. 🚪

🦋 Vcf parser 🦋

(yes that's the whole line. she's a section header. she's mysterious. we respect her.)

👑 AUTHOR 👑

this manpage was written by Nilesh Patra for the Debian distribution and can be used for any other usage of the program. ty for your service, legend. 🫡

and that's the whole page bestie!! no notes, ate and left no crumbs. 💖

bio-vcf 0.9.5 — September 2021 🌸 (that's the version and the date, folded into a cute lil sign-off instead of a boring footer line, you're welcome 🎀)