Haplotype Blocks Identification Based On Several Snps

Question

[vlata119]

Dear all!

I'm working on the following task. Our lab guys have genotyped a couple of SNPs related to a particular disease. I need to reconstruct haplotype blocks consisting of those SNPs.

Plink software, http://pngu.mgh.harvard.edu/~purcell/plink/, seems to be an appropriate solution, but I get stucked with it. Still haven't tried other software solutions like Haploview, Beagle, etc...

Any suggestions are highly appreciated!

Mvh, vlata119

[Zev.Kronenberg]

Do you have pedigree data or unrelated individuals? Where do you get stuck in plink?

[keyuxu_2017]

only for unrelated individuals. Does it fit for Plink software? or any other package you recommend?

Answer 1

[anin.gregory]

You should read: Jeffreys, A.J., L. Kauppi, and R. Neumann, 2001. Intensely punctated meiotic recombination in the class II region of the major histocompatibility complex. Nature Genetics 29: 217-222. This paper is foundational to your work.