Best Way To View Haplotypes In Non-Human Organisms?

Question

[Rubal]

Dear all,

I have genome-wide snp data from non-human organisms and would like to find a good way to visualise haplotypes/LD blocks. I have tried using haploview but it does not seem amenable to the use of non-human data, at least I have not succeeded in getting it to work so far. Does anybody know of a good way to visualise haplotypes with non-human sequence data?

Thanks in advance for any suggestions,

Rubal

[Pierre Lindenbaum]

what's wrong with haploview ?

[Larry_Parnell]

I agree with Pierre - it would be good to know some details on why it does not work for you. A stand-alone version of Haploview should support your objectives if the organism is diploid.

[Rubal]

it seems to ask for which chromosome i am mapping (from human reference) also as an aside it gives an error when I try and upload my data, though people in my group have had the same problem with human data, so that is a problem with our input not the program. Has anyone used haploview succesfully with non-human data?

[Rubal]

Ok I can try again with haploview, though out of interest (and encase haploview isnt working), can anyone recommend any good alternatives if they exist?

[Rubal]

I have the 3 input files in phase format, if anyone has time I can send a sample and someone could point out what's wrong with them- haploview wont accept it.

[Larry_Parnell]

If you have no pedigree info, and this is likely, then this field should be zero. Haploview should work with human and other data.

[William]

How did you get your variant calls into the 3 input files needed for Haploview?

Answer 1

[Larry_Parnell]

We use Haploview (sometimes) and GoldenHelix's HelixTree (mostly) to view haplotypes and LD blocks.

[Rubal]

thanks, I looked into GoldenHelix but I don't think our lab will pay for the software

[Rubal]

Thanks that's good to know