Man pages sections > man1 > bref

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

Bref(1) General Commands Manual Bref(1)

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).
 
June 2016 4.1