Almost all procedures in HIBLUP support to filter samples or SNPs of interest in analysis, there are total four options available to accommodate the different requirements from users:
--keep: to specify a file listing the individuals which will be used in analysis;--remove: to specify a file listing the individuals which will be removed in analysis;--extract: to specify a file listing the SNPs which will be used in analysis;--exclude: to specify a file listing the SNPs which will be removed in analysis.
Please see file format here.