Haplotypes from SNP data

Question

[admamajdi]

Hello,

I want to generate haplotypes from SNP data such that for example I could use 4 SNPs to create a haplotype and so on.

Any idea how to get this done and if there is any software that it can be used for this?

Thanks!

Answer 1

[Charles Warden]

I've done some testing with HLA haplotypes, and phasing is supposed to help with defining SNP chip data.

I am not sure about what publication to currently list, but I think a sufficient number of SNPs probably can give reasonable haplotype assignments (at least when haplotypes are sufficiently different, and quality of the assemblies are relatively clear - or at least well characterized in independent studies).

So, my guess is that you may probably want to have more than 4 SNPs, but I think the specifics will vary from project to project.