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SNP data for polyploids

Posted: Thu Nov 17, 2016 5:57 pm
by mghanbari
Hi all,
I am curious to know how can i define SNP data in a tetraploid crop like potato which is heterozygote and has the possibility out of 5 different genotyping types. AAAA, AAAa,AAaa, Aaaa,aaaa.
also please help me how can i deal with "sex" index when the SNP data come from plant.


Thanks in advance,

Re: SNP data for polyploids

Posted: Wed Nov 23, 2016 12:02 pm
by lckarssen
As far as I know, GenABEL was developed with human genomes in mind. I would have to double check, but I'm quite sure there is no option for polyploids.

Re: SNP data for polyploids

Posted: Tue Dec 13, 2016 7:11 am
by Ritchie
mghanbari wrote:Hi all,
I am curious to know how can i define SNP data in a tetraploid crop like potato which is heterozygote and has the possibility out of 5 different genotyping types. AAAA, AAAa,AAaa, Aaaa,aaaa.
also please help me how can i deal with "sex" index when the SNP data come from plant.


Thanks in advance,


I think it would be possible with some modifications.

Re: SNP data for polyploids

Posted: Tue Dec 13, 2016 8:26 am
by lckarssen
Ritchie wrote:I think it would be possible with some modifications.

Of course. With modifications it would work. However, given that this goes down to the level of the data model, it won't be "some" modifications. It will be quite some work because many (all?) functions in the GenABEL package would need to be updated.

GenABEL is open source software, so feel free to contribute! Currently the source code is in the R-forge SVN server, but if you're serious about contributing patches and would prefer Github or BitBucket that can be arranged.
I would be willing to help where I can. And if you don't have the time or skills yourself you could commission my company (PolyOmica). We would be happy to discuss the options.