Hello. I have a list of 54 tagging SNPs. And I would like to get a list of all SNPs in LD with each one of my 54 SNPs. I think I need some kind of software that would allow me to get all correlated SNPs using r2>=0.6 or 0.8.. I cannot find a way to do this sistematically for 54 SNPs.. Can anyone help? Thanks
PLINK can do this:
"to obtain all LD values from a group of SNPs with other SNPs, use the command --ld-snp-list mysnps.txt where mysnps.txt is a list of SNPs."
rAggr can find SNPs and indels in LD with your list of SNPs. See: http://raggr.usc.edu/
It now has data from 1000 Genomes Phase 3 and can search up to 5Mb in each direction from the queried SNP.
SNAP Proxy search is the one I have been using, it is easy to use, they should update to hg19!
If you can pull the SNPs out of the 1000 Genomes VCF, you can then run vcf-tools --hap-r2 or something suitable. If the SNPs are close together, you can use the fully-phased VCF and --hap-r2. Otherwise you may need to use --geno-r2, which is probably what you want anyway. Good luck.
May be SNAP (http://www.broadinstitute.org/mpg/snap/ldsearch.php) is the tool you need.
The problem using PLINK is that you need to have the full list of genotypes for all possible SNPs. From the question (correct me if I am wrong) I assume you have several SNP names (probably with rs as they are tag SNPs so they should be known and previously genotyped), and you want a list of possible correlated SNPs in certain population similar to yours, and you have not genotyped them yet.
For this kind of task you have several option, the ones I have used before when I was at Sanger are:
GLIDERS (unfortunately it is not up to date with 1000 genomes, only HAPMAP projects)
[http://www.sanger.ac.uk/resources/software/gliders/][1]
EnsemblAPI (I think that you can do that now in the web, probably you could ask the help-desk team, they are very helpful)
[http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#ld][2]
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I am getting "A server error occurred. Try submitting again. If you still receive an error, contact the site administrator" while trying to query LD for marker SNP's .
Were you able to resolve this ?
Hi, I used this https://analysistools.nci.nih.gov/LDlink/ for calculating LD. Thanks