---
name: "bref3"
section: "1"
platform: "linux"
package: "beagle"
version: "241217-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/bref3"
---

# bref3(1)

Tool for compressing diploid reference VCF files for the Beagle program.

## NAME

Bref - Tool for compressing diploid reference VCF files for the Beagle program.

## SYNOPSIS

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

## DESCRIPTION

Bref is a tool for compressing diploid reference VCF files.\
 Beagle performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection. Genotypic imputation works on phased haplotypes using a Li and Stephens haplotype frequency model. Beagle also implements the Refined IBD algorithm for detecting homozygosity-by-descent (HBD) and identity-by-descent (IBD) segments.

## 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".

- **bref**=*filename*

  Prints a .vcf file to standard out.\
   Specifies a binary reference file. The filename should end in ".bref".

## SEE ALSO

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

## AUTHOR

Beagle and Bref were written by Brian L. Browning.

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