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

       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).

4.1                                                 June 2016                                            Bref(1)

       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.

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

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".

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

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