Use artificial F1 vcf to run XP-CLR for selfing species?

[hungweichen0327]

Dear @hardingnj and community,

I would like to ask whether it's better to use the artificial F1 vcf file to run XP-CLR for selfing species.

For some crop species, they are self-pollinated (Thus, the heterozygosity of the genome is low). Do I need to generate the artificial F1 vcf file in each population before running XP-CLR?

Example way of generating artificial F1 vcf file:
Assume there are 6 samples in the population A. The first allele of sample 1 and the second allele of sample 2 will be merged per site. Finally, there are 3 artificial samples in the vcf file of population A.

Thank you for the help.