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How To Reconstruct Haplotypes And Visualize Them In Haploview

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.

ld haplotype
• 4,620 views • link
updated by Zev.Kronenberg Zev.Kronenberg • written by mary mary

2 answers

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.

• 3 views • link
written by Genotepes Genotepes

Haploscope is also worth checking out:

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

• 0 views • link
written by Zev.Kronenberg Zev.Kronenberg

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