Hi everyone, I'm new to this software and to this forum, I would need to estimate the linkage disequilibrium using my data. I have around 3000 individuals with a list of SNP genotyped and imputed. I would like to create a LD plot from my population. I would like to do this on a small region of around 100kb. my file is in this format:
Subjects SNP1 SNP2 SNP3 SNP4 A01 0.02 0 0.5 ... A02 0.45 1 0.57 ... A03 1.6 2 0.3 ... .... .... ... ... ...