HIBLUP can help to transform the genotype in binary format into another type, for examples, additive coding format, dominance coding format, and the acceptable format of BLUPF90 software. If you are really struggling with transforming genotype into certain format which can not be accomplished by publicly available tools, please contact us and we are pleased to achieve it in HIBLUP.
Additive coding format
Use the following commands to transform binary genotype into additive coding format:
./hiblup --trans-geno
--bfile demo
--add
--out add_coding
A file named “add_coding.geno.A.txt” will be generated in the work directory, overview of the file:
ID M1 M2 M3 M4 M5 IND0701 2 1 1 1 0 IND0702 1 0 1 1 0 IND0703 0 2 0 0 0 IND0704 1 1 1 1 0 IND0705 1 0 0 1 0
Dominance coding format
Use the following commands to transform binary genotype into dominance coding format:
./hiblup --trans-geno
--bfile demo
--dom
--out dom_coding
A file named “dom_coding.geno.D.txt” will be generated in the work directory, overview of the file:
ID M1 M2 M3 M4 M5 IND0701 0 1 1 1 0 IND0702 1 0 1 1 0 IND0703 0 0 0 0 0 IND0704 1 1 1 1 0 IND0705 1 0 0 1 0
BLUPF90 acceptable genotype format
Use the following commands to transform binary genotype into the acceptable genotype coding format of BLUPF90:
./hiblup --trans-geno
--bfile demo
--blupf90
--add # or '--dom' for dominance effect
--out bf90
A file named “bf90.geno.A.txt” will be generated in the work directory, overview of the file:
IND0701 211100111001 IND0702 101101011001 IND0703 020000001000 IND0704 111100001000 IND0705 100100111000