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Question: find LD of list of SNPs, located on different chromosomes
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gravatar for anamaria
12 months ago by
anamaria • 80
anamaria • 80 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

ld snps list different chromosomes • 407 views
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modified 12 months ago by toralmanvar • 830 • written 12 months ago by anamaria • 80
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gravatar for toralmanvar
12 months ago by
toralmanvar • 830
toralmanvar • 830 wrote:

You can use PLINK for the same.
ADD COMMENT • link written 12 months ago by toralmanvar • 830

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

ADD REPLY • link written 12 months ago by anamaria • 80

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 REPLY • link written 12 months ago by toralmanvar • 830
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