I want to do LD analysis on my data (Illumina BovinSNP50 BeadChip) by plink
I have two problem :
1- the pedigree of my data are very crowded and I don't know if I put zero for parental and maternal column in ped file, i can trust to my result or not. because, as you know in livestock population we have a many relationship and it affected the LD extent and pattern
2-in Ped file, what can I put in phenotype column? I know if I put zero I can use --no-pheno in plink. but i have EBV for many traits such as, EBV for milk production, protein percentage and ....
Is there any one who can help me?