How To Reconstruct Haplotypes And Visualize Them In Haploview

Question

[mary]

Dear all

I genotyped data from 1500 animals by 50K chips, and now I want to use haploview for block analysis. Do I need to reconstruct haplotype before insert to haploview? If reply is yes, which software (except fastphase) I can use?

More information is that i don't have pedigree for animal.

Answer 1

[Genotepes]

Hi

as far as I remember, Haploview is applying a EM algorithm on haplotype blocks (blocks are determined by techniques not related to whole region haplotyping). So you can upload your data in Haploview and you'll get information about blocks.

Answer 2

[Zev.Kronenberg]

Haploscope is also worth checking out:

http://www.ncbi.nlm.nih.gov/pubmed/22147662