Entering edit mode
2.6 years ago
?
▴
60
I'm trying to do LD pruning with PLINK but I can't find any proper documents about the algoritm used. There are options as indep, indep pairwise and indep pairphase and suboptions as windowsize, stepsize and threshold. I'm not sure what each means and which options to choose. Since I'm a newbie, to me indep sounds like 'choose set of snps which are independent to each other and which are the largest in number' and indep-pairwise sounds like 'choose snps if it at least has one snp which is independent to it'
I'm really lost. could someone please explain what these are about or suggest me a documentation to read about it?
