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[SOLVED] Get LD data for any two SNPs

Is there a good way to take any two SNPs and pull out the LD between them, particularly the R-squared and the directionality of the linkage (e.g. A in SNP1 occurs with G in SNP2 95% of the time)?

Obviously I can do this manually, but I am wanting to do it for a list of several thousand SNPs, so I am hoping for a scalable solution. Right now I can't find anything, and it looks like I will have to come up with my own solution using vcftools and the 1000 genomes data.

Thanks!

genome linkage disequilibrium
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updated by Raju • Raju • written by Mike Dacre • Mike Dacre

Yes! It looks like that does work, I am not sure how many queries their API can tolerate, but I am going to try this tonight to see. I also want to compare this to running the calculations with plink/vcftools to see which is faster/more stable. Thanks!

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written by Mike Dacre • Mike Dacre

plink1.9 offers this functionality, as answered by @chrchang523

In case anyone else wants to do this, I wrote a little package based on plink and LDlink that allows many-to-many LD lookup. Basically, provided two SNP lists, it creates a list of SNP LD pairs between each SNP in the first list and every SNP in the second list, filtered by distance and R2. Provided a first list of 40,000 SNPs and a second list of ~10million risk alleles it runs in a couple of hours.

The output includes phase SNP data to ask the question: 'given Allele X in SNP A, what is the allele in SNP B' for every single possible pair.

All of this is just done by some basic math, running plink a bunch of times, and parsing the output. Hopefully it helps someone else.

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written by Mike Dacre • Mike Dacre

Hi Mike,

I have exactly the same issue like you and I would like to use your code to compare LD between two lists of SNPs. Can you please tell me where I can find that code?

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written by anamaria anamaria

3 answers

"plink --r2 in-phase" provides both r-squared and directionality; see https://www.cog-genomics.org/plink/1.9/ld#r .

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written by chrchang523 chrchang523

The ensembl REST API offers this function http://rest.ensembl.org/documentation/info/ld_pairwise_get

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written by cmdcolin cmdcolin

Thanks! That is great, but unfortunately it doesn't include the directionality, what I really need to know is what SNP2 is given some value for SNP1 (i.e. SNP2 is T 90% of the time when SNP1 is G)

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written by Mike Dacre • Mike Dacre

I see! Perhaps the ensembl team would be interested in adding that function.

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written by cmdcolin cmdcolin

You can do this using the below command: you need to have a bim, bed and fam files

plink --bfile Obesity_Send --allow-no-sex --extract SNPs.txt --r2 --out LD_file
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written by Raju • Raju

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