I study about ROH in some sheep breed. I want to found ROH in 1-3, 3-6, 6-12, 12-18, >18 category. for long ROH I need to correction for missing and hetro genotype. for example:
I need to allow one hetrozygot and 3 missing genotype on ROH segment with more than 16 Mb lenght. dose any body know how can I do this ?
I use following command:
plink --homoyg-snp 40 --homoyg-gap 1000 --homoyg-window-snp 50 --homoyg-density 100