I have a list of SNPs, around 385, located on different chromosomes, and I want to obtain the LD between all of them.
You can use PLINK for the same.
can you please explain how would I do that using plink?
Supposing that you have vcf file for the SNPs, you can use following command:
plink --file your_data.vcf --r2 --out out_LD.txt
You can also provide additional options based on your need, like mentioned in this post.