Different with other software, the phenotype file required for HIBLUP should include not only the phenotypic records, but also the environmental covariates, fixed and random effects. The first column must be the individual id, header should be included in the file. Brief view of example phenotype file is as follows:
id sex season day weight loc dam tr1 tr2 tr3 Ind1 F Winter 100 2.9 l3 Ind902 73.9776 21.3252 35.7737 Ind2 M Summer 100 1.5 l2 Ind902 94.1994 19.1162 54.2453 Ind3 M Winter 100 1.8 l4 Ind903 88.6698 5.9538 71.0284 Ind4 M Winter 100 1.9 l1 Ind903 87.0458 -2.8179 37.2703 Ind5 M Spring 100 2.2 l3 Ind905 68.8077 2.5357 59.5402 Ind6 F Autumn 100 1.9 l1 Ind905 85.9242 -3.06 48.4822
Any symbol below will be treated as missing when loading the file:
NA Na . - NaN NAN nan na N/A n/a <NA>
The file should be assigned to the parametric option --pheno.
By default, HIBLUP will take the trait at second column for analysis, users can specify a different column by using --pheno-pos n, for example, --pheno-pos 8 represents using the 8th column for analysis.
NOTE
If there are multiple traits to be used for estimating genetic correlation, please use space as separator, e.g. --pheno-pos 8 9 10.