HIBLUP can filter the sample and SNPs in analysis for all available functions, the file is easy to prepare, just list the name of individual or the id of SNP in file with no header.
Example file id.txt:
Ind16 Ind56 Ind110
if users are supposed to remove those individuals in analysis, just assign it to flag --remove. Contrarily, if it is assigned to flag --keep, only those individuals in file will be used for analysis.
Example file snp.txt:
SNP23 SNP198 SNP432
if users are supposed to remove those SNPs in analysis, just assign it to flag --exclude. Contrarily, if it is assigned to flag --extract, only those SNPs in file will be used for analysis.