create an haplotype

Question

[marmar]

Hi to everyone! I'm an italian student and I don't speak very well english so, I apologize for the language. We found, with NGS, a pathogenetic variant (eterocompound in the same gene) in patients with the same country of origins; now we would like to know if this variant is a founder mutation or not. On this thesis I will have to create an hyplotype from variant and SNPs: how can I do it? Thanks for helping, unfortunately I'm not very experienced with this work.

Answer 1

[mansar_76]

You can select the additional variants flanking the identified mutation and construct haplotype to see if all patients carry similar haplotype. Additional variants can be selected from e.g 5Mb region on each side and haplotype can be constructed with Merlin. These predicted haplotype can be viewed with haplopainter. I hope this is helpful but more information can be helpful to give additional suggestions.