Shared Haplotye In Specific Region Based On Family Based Study

Question

[Omid]

I have done 300K SNP array by Illumina for 27 patients and found a common deletions in 9 of them. Now I would like to study shared haplotype in this specific region in these 9 patients. How do I do it in easier way? Which program is better and how can I do it? I tried shared haplotype by plink but it is base on case-control and I am working on family-based study.Thanks

Answer 1

[Zev.Kronenberg]

Have you tried GeneHunter or MapMaker3 from the Broad institute?

http://www.broadinstitute.org/scientific-community/software?criteria=Linkage%20Analysis