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find LD of list of SNPs, located on different chromosomes

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
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updated by Tm Tm • written by anamaria anamaria

1 answer

You can use PLINK for the same.

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written by Tm Tm

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

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written by anamaria anamaria

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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written by Tm Tm

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