Question: find LD of list of SNPs, located on different chromosomes
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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 14 months ago anamaria • 40 • updated 14 months ago toralmanvar • 760
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You can use PLINK for the same.

ADD COMMENTlink 14 months ago toralmanvar • 760
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can you please explain how would I do that using plink?

ADD REPLYlink 14 months ago
anamaria
• 40
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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.

ADD REPLYlink 14 months ago
toralmanvar
• 760

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