HIBLUP has the function of predicting genomic estimated breeding value (GEBV) or genomic polygenic risk score (GPRS) using the pre-computed SNP effects and individual level genotype data, which is the same with the function “--score” in PLINK software, but several times faster for computing.
The command to do prediction is as follows:
./hiblup --pred
--bfile demo #the binary genotype data
--score demo.snpeff #the pre-computed SNP effects
--threads 10
--out demo
Note that the genotype should be in PLINK binary file, and at least 5 columns should be included in SNP effects file (see detailed format here). By default, HIBLUP codes the genotype in additive genetic effect (i.e., 0 1 2 for AA Aa aa), user can add a flag “--dom” to code the genotype in dominant effect (i.e., 0 1 0 for AA Aa aa) if the provided SNPs effects are all in dominant. But if both “--add” and “--dom” are specified in commands, the SNP effect file must have 6 columns, of which the 5th and 6th are the additive and dominant SNP effects, respectively. Thus, if there are additive and dominant effects in file, please remember to add flag “--add --dom” in the commands.
A file named “demo.bv” will be generated in the work directory, overview of this file:
id trait1 trait2 Ind2 -0.305403 2.6644 Ind5 0.00897198 -1.36166 Ind11 0.392148 -0.653216 Ind17 0.00232218 -0.213599 Ind22 -0.359507 -2.12692 Ind45 -0.232806 0.269005
As shown above, the first column is the individual id, and the rest of columns are the predicted GEBV or GPRS, the number of columns depends on the number of effects provided in SNP effects file.