Question: Pairwise Snp Ld Scoring
3
gravatar for Radhouane Aniba
2.2 years ago by
Radhouane Aniba720 wrote:

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
ADD COMMENTlink written 2.2 years ago by Radhouane Aniba720
1

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?

ADD REPLYlink written 2.2 years ago by jvijai960

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

ADD REPLYlink written 2.2 years ago by Larry_Parnell15k

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.

ADD REPLYlink written 2.2 years ago by Radhouane Aniba720

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 ?

ADD REPLYlink written 2.2 years ago by Radhouane Aniba720
4
gravatar for Larry_Parnell
2.2 years ago by
Larry_Parnell15k
Boston, MA USA
Larry_Parnell15k wrote:

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.

ADD COMMENTlink written 2.2 years ago by Larry_Parnell15k
3
gravatar for jvijai
2.0 years ago by
jvijai960
jvijai960 wrote:

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

ADD COMMENTlink modified 2.0 years ago • written 2.0 years ago by jvijai960

Good choice. We also use SNAP for some projects.

ADD REPLYlink written 2.0 years ago by Larry_Parnell15k
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