Question: find LD of list of SNPs, located on different chromosomes
0
gravatar for anamaria
12 months ago by
anamaria80
anamaria80 wrote:

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

ADD COMMENTlink modified 12 months ago by toralmanvar830 • written 12 months ago by anamaria80
0
gravatar for toralmanvar
12 months ago by
toralmanvar830
toralmanvar830 wrote:

You can use PLINK for the same.

ADD COMMENTlink written 12 months ago by toralmanvar830

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

ADD REPLYlink written 12 months ago by anamaria80

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.

ADD REPLYlink written 12 months ago by toralmanvar830
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