Bref - Tool for compressing diploid reference VCF files for the Beagle program.
java -jar /usr/share/beagle/bref.jar [
vcf]
or
java -jar /usr/share/beagle/bref.jar [
bref]
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.
-
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
Beagle and Bref were written by Brian L. Browning.
This manual page was written by Dylan Aïssi <
[email protected]>,
for the Debian project (but may be used by others).