Pairwise SNP LD scoring

Question: Pairwise SNP LD scoring

Hello everyone,

I have two lists of SNPs, List A and List B, I want to calculate r2 of each SNP in A with each SNP in B in a pairwise manner.

None of the tools I know allow that, I can play with awk to create a single file with all pairwise pairs but then I am wondering which tool could be the best to give the generated file as Input, plink ? the problem with plink is that I never understood what is the my data file is, like in this command

plink --bfile mydata --ld rs2840528 rs7545940

Any idea is welcome

Cheers Radhouane

snp r

created 15 months ago by Radhouane Aniba 690•1•8

Which tools did you try? In which (reference) population do you wish to calculate the LD?

Well I tried SNP which is good because it allows to extend a SNP list, I am interested in CEU population, but the problem is that I want to use the same features but not for a predefined tagSNPs, I have my own list.

http://pngu.mgh.harvard.edu/~purcell/plink/ld.shtml#ld2 shows an example of how to do this. Do you have genotype data or just a list of SNPs? If only SNPlist, do you know the ethnicity to use a comparable Hapmap population?

I have just a SNPlist, for CEU population where do I get genotypes and how to format this my data file they have in the example, how to format a per file ? what it contains ?

2 answers

We use Haploview. It is free and one of if not the best for this. It should be easy for Haploview to take you list of SNPs as a single file, after which you can look for the LD between distinct pairs.

To calculate LD with accuracy, you need genotypes from at least 50 unrelated individuals.

created 15 months ago by Larry_Parnell ♦ 14,180•7•25

You can use SNAP from Broad to get pairwise LD between two SNPs or a list of SNPs.
You can also find other SNPs that are in LD (proxySNPs) for your SNPs. You can use specific populations, (different hapmap datasets including 1000genomes).
You can also find if those SNPs have membership in major commercial array platforms. I use it all the time and like it very much.
http://www.broadinstitute.org/mpg/snap/ldsearchpw.php

created 13 months ago by jvijai 930•1•8

updated 13 months ago by jvijai

Good choice. We also use SNAP for some projects.