Hi all,

I am working with Wolbachia genomic data. I am interested in looking at loci associated with specific environmental co-variates. Before i do the g x e scans, I wanted to LD prune the SNPs (n=593). I calculated LD decay, and it is pretty high (average genome wide r >0.75) across the genome. How would one go about pruning LD and to filter SNPs? Specifically, how would you set window size or a LD cut-off for something clonal for bacteria?

Thanks in advance!