Background: I am a grad student doing eQTL analysis and just starting to dip my feet into plink. From what I understand, LD pruning is typically done by the '--indep-pairwise option'. Additionally, I can use the '--show-tags all' option to keep track of the pruned SNPs.
Thing is, I came across a tutorial highlighting why clumping is preferred over pruning (https://privefl.github.io/bigsnpr/articles/pruning-vs-clumping.html). I believe I understand the limitation with pruning (e.g. a situation where many SNPs are prune may arise, creating larger-then intended regions with no SNP representation). That being said, I am quite confuse about how clumping works and simply looking for more material to read on. For instance, I don't understand what the association test is calculating and how that is being used in the clumping procedure (according to the tutorial, there is some MAF statistic being used, but that statistic isn't present in the association file I created). I'm also having difficulty understanding how the index variant and clump variant are used.
Perhaps I am going down a rabbit hole that I shouldn't be concerned with based on my eventual goal (eQTL). But was hoping someone could recommend some resources comparing the two approaches.