need help with LD calculation with imputed genotypes

Question

[air.chuan.1987]

Hi guys,

I need to calculate pairwise LD in a list of SNPs using our imputed genotypes. Anyone knows what is the easiest way of doing that? I used to convert imputed genotypes into best guess and use PLINK but that doesn't seem to be the most correct approach. Any suggestions? Thanks a lot!

Thanks, Charlie

Answer 1

[Shab86]

Would these help?

• How To Use Plink To Compute The Ld Between Two Sets Of Snps?
• Pairwise Snp Ld Scoring