Question: Best Way To View Haplotypes In Non-Human Organisms?
4
gravatar for Rubal
8.1 years ago by
Rubal80
Rubal80 wrote:

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

linkage non haplotype haploview snp • 2.7k views
ADD COMMENTlink modified 6.1 years ago by Biostar ♦♦ 20 • written 8.1 years ago by Rubal80
1

what's wrong with haploview ?

ADD REPLYlink written 8.1 years ago by Pierre Lindenbaum124k

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.

ADD REPLYlink written 8.1 years ago by Larry_Parnell16k

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?

ADD REPLYlink written 8.1 years ago by Rubal80

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?

ADD REPLYlink written 8.1 years ago by Rubal80

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.

ADD REPLYlink written 8.1 years ago by Rubal80

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

ADD REPLYlink written 8.1 years ago by Larry_Parnell16k

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

ADD REPLYlink written 6.1 years ago by William4.5k
1
gravatar for Larry_Parnell
8.1 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

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

ADD COMMENTlink written 8.1 years ago by Larry_Parnell16k

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

ADD REPLYlink written 8.1 years ago by Rubal80

Thanks that's good to know

ADD REPLYlink written 8.1 years ago by Rubal80
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