I have discovered and genotyped thousands of SNPs through NGS technologies for doing population genetic analyses. Now I have to determine which SNPs are linked (determine LD); for that purpose, when working with less SNPs, I used to use genepop, and I can continue using it now. But I would be very acknowledged if any of you could tell me a software package for doing this more efficiently.
The major problem comes when trying to get the LD phase... I was used to do this with PHASE software, but it requires a lot of manual work that, nowadays with thousands of LD pairs I cannot afford. So, what software would you recommend me?
P.s: I am working with a non model organism.
I personally use phase and the R package genetics. If you can program in R you can convert your SNPs in the proper format. I have written something to go from a SNP table to phase and/or genetics. I see no way to do this quickly without some programming skills (perl and python would do as well, and actually they would probably be better!)
ok, that's for phasing the snps, but what about knowing which snps are in LD? Is that what you mean R-genetics package for?
Thanks
Well, actually when you phase the SNPs you can calculate LD in a deterministic way (there are formulas for that). As an alternative you might (as I do) use the R genetics package to calculate LD
ok
i am sorry because of the missunderstood but, i have always thought that first one should get the LD (to see which snps are linked) and then, phase LD positive snps (as a single marker) to get the phased genotype.
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