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).