I would like to compute LD (r2) between ALL my SNP pairs.
I think running the default
plink --file mydata --r2 applies some pre-defined filtering as below:
--ld-window 10 --ld-window-kb 1000 --ld-window-r2 0.2
The explanation for these arguments makes no sense whatsoever. So I ended up using Mapthin to thin my SNPs.
Now that I have my short SNP set, all I want to do is compute r2 values between ALL my SNPs pairs without any filtering. How do I accomplish that?