Haplotype Sharing Analysis With Illumina/Affymatrix Snp Data

Question

[User 1793]

Hi,

I need to make a haplotype sharing analysis in population Genetics. I have with me an illumina humanhap 650K data of 10 populations.

Please help.

Thanks

Answer 1

[Genotepes]

Hi

we would need slightly more information about your project (at least I do need).

Are you looking for regions that are shared between populations (I guess long segments) ? Do you need to evaluate genetic distance between populations (you will need anyways) ?

Haplotype clustering is quite generic although it is also a keyword for studies like the one implemented in HapCluster (other methods exist). However, these methods usually look for excess of haplotype sharing in cases as opposed to controls...

So definitely we would need more information

Christian

[User 1793]

thanks for your reply. I have a data of 10 populations from Africa to Australia, I have phased it and broken chromosomewise, and now I need such script which can work with variable window (5kb to 500kb) and look for the shared segments in all these populations. for example if at chromosome 1, I break the data in to 5kb length then I need to find out that how many segments are shared among all the populations. I hope it explains my need. thanks