I have a population with 1066 bulls that just sire was genotyped by Illumina Bovine SNP50K BeadChip . my data is not trios, just in some animal, father and son was genotyped, but I have pedigree for all animals. I used plink for calculate r2 chromosome by chromosome in first step. as I am new in LD analysis, i confused in analysis , I want to know:
1- is pedigree important in this data analysis?
2- how can i calculate D' for my data?
3- when I used plink for haplotype reconstruction (phasing) as a command "plink --bfile mydata --blocks " the file that it gave me was empty??!?! i don't know its correct or not?
is there any one that can help me?