SNPs effect file is used for predicting GEBVs of genotyped individuals or implementing genomic mating, at least 5 columns are required, an example is as follows:
SNPid a1 a2 freq_a1 add dom SNP1 A C 0.1243 0.30134 0.00000 SNP2 G T 0.0345 -0.06324 0.00124 SNP3 A G 0.3635 0.15425 -0.00913
The file should be assigned to parametric option --score.
NOTE
As mentioned before, the provided type of SNP effect should be consistent with the flag --add and --dom, and the column of additive SNP effect should be at the front of dominant SNP effect if both of them are provided.