bref1

Tool for compressing diploid reference vcf files for the beagle program.

Usage

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

or

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

Overview

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".