Bref(1)

📦 version 250227, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 BREF(1) — the manual, but make it cute 💖

okay bestie, pull up a chair, we're learning Bref today and honestly? it's giving "small tool, big slay" 🧚

✨ NAME ✨

Bref — a tool for compressing diploid reference VCF files for the Beagle program. that's it, that's the whole job, and she does it gorgeously 💅

🌸 SYNOPSIS 🌸

java -jar /usr/share/beagle/bref.jar [vcf]
or
java -jar /usr/share/beagle/bref.jar [bref]

two moods, one jar file, no notes.

🦋 DESCRIPTION 🦋

so Bref is a tool for compressing diploid reference VCF files. that's the main character move ✨

now, Beagle (her sister, her icon, her moment) performs:

  • genotype calling
  • genotype phasing
  • imputation of ungenotyped markers
  • identity-by-descent segment detection

and the way genotypic imputation works? it's on phased haplotypes, using a Li and Stephens haplotype frequency model. no cap. 👑

Beagle also implements the Refined IBD algorithm for detecting homozygosity-by-descent (HBD) and identity-by-descent (IBD) segments. she's multifaceted, she contains multitudes 💜

🎀 OPTIONS 🎀

  • vcf=filename — creates a .bref file ✨ specifies a VCF file with phase, non-missing genotype data. if the VCF file is a text file, its filename should end in ".vcf". if the VCF file is GZIP-compressed, its filename should end in ".vcf.gz". okay so the extension is not a suggestion, it's a vibe check, respect it 🙈
  • bref=filename — prints a .vcf file to standard out 📤 specifies a binary reference file. the filename should end in ".bref". periodt.

🔥 SEE ALSO 🔥

https://faculty.washington.edu/browning/beagle/beagle.html

go read it, bestie, it's lowkey iconic 📚

💜 AUTHOR 💜

Beagle and Bref were written by Brian L. Browning. absolute legend, we stan 🫶

This manual page was written by Dylan Aïssi <bob.dybian@gmail.com>, for the Debian project (but may be used by others). sharing is caring, fr fr 💚

🌈 and that's the whole page!! every flag, every filename, every algorithm, all accounted for. nothing skipped, nothing invented, just facts with better energy ✨

version 4.1, from June 2016 — yes she's an older queen but she still ate 💅 mwah, bye bestie!! 🍓

📦 where this page comes from