Hi everyone.
I am hoping you can help me. I am new to the whole concept of linkage disequilibrium and using Plink to calculate this for my dataset. I have 4 individuals (family members) of mixed ancestry, and i want to calculate the linkage disequilibrium for all snps across the genome of these individuals. Is this possible? and how would i go about doing this? would i need to merge my data with that of the AFR populations in the 1000 genome (phase3) data set for example? or would I just make use of LD-prunning? Do I do the QC steps suggested by some tutorials online, like the hwe, missing and maf filtering steps prior to the LD calculations, or can I just jump right into the LD calculations. So in my mind, I am hoping to find potential 'disease-causing' snps that are in LD with my candidate-gene snps. if that makes sense. I am not sure if the above even makes sense, but if anyone can shed some light, I would really appreciate it.
