I am going to conduct a Genome Wide Association Study using bumblebee genome data and I am planning to use PLINK for that. Due to haplodiploidic nature of the sex determination system of the species(bumblebee) the males are haploid and females are diploid. However, I am dealing with genome datasets of males (haploid genome). I was wondering what would be the best strategy to use PLINK in this case? PLINK manual says " for haploid chromosomes, genotypes should be specified as homozygotes''. I was wondering if someone has used the technique previously to deal with ploidy issue? Any suggestion/recommendation for a specific toolset for conducting GWAS with haploid genome data will be highly appreciated too.