find LD of list of SNPs, located on different chromosomes
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3.0 years ago
anamaria ▴ 160

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 • 1.0k views
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3.0 years ago
Tm ★ 1.0k

You can use PLINK for the same.

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

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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.

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