Question: find LD of list of SNPs, located on different chromosomes
0
gravatar for anamaria
4 months ago by
anamaria0
anamaria0 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 4 months ago by toralmanvar750 • written 4 months ago by anamaria0
0
gravatar for toralmanvar
4 months ago by
toralmanvar750
toralmanvar750 wrote:

You can use PLINK for the same.

ADD COMMENTlink written 4 months ago by toralmanvar750

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

ADD REPLYlink written 4 months ago by anamaria0

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 3 months ago by toralmanvar750
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