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?
1 - Pedigree is not important in LD analysis, but will, as Zev told you, inflate LD estimates. Recently, an [R] package LDcorsSV (Mangin et al., 2011, Heredity) taking into account Kinship and/or population structure was released. You may try it. A bit long computing time but it works.
2 - You can use different softwares to compute LD estimation but check for which estimates is the most appropriate one (D', r, r2). One of the most used software is 'Plink!' but you can also use 'Tassel' for example.
3 - The bfile option in Plink needs a special format if I remember well.
1- I prefer don't include the pedigree, because I want compare two breed that for second breed i don't have pedigree.
2- I think the plink just calculate r and r2. i can do haploview, but i don't know I need do haplotype reconstruction before input data to haploview or not? (i can do haplotype Reconstruction by fastPHASE), but plink is easy and fast
3- I did plink --file mydata --make-bed --out mydata, so i had special format for do blocks command. but i didn't understand why plink doesn't do that?
