find LD of list of SNPs, located on different chromosomes

Question

[anamaria]

Hi,

I have a list of SNPs, around 385, located on different chromosomes, and I want to obtain the LD between all of them.

Please advise, Thanks Ana

Answer 1

[Tm]

You can use PLINK for the same.

[anamaria]

can you please explain how would I do that using plink?

[Tm]

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.