SNP data for polyploids

Questions about GenABEL (aka *ABEL) suite of packages
Forum rules
Please remember not to post any sensitive data on this public forum.
The first few posts of newly registered users will be moderated in order to filter out any spammers.

When get a solution to the problem you posted, please change the topic name (e.g. from "how to ..." to "[SOLVED] how to ..."). This will make it easier for the community to follow the posts yet to be attended.
mghanbari
Posts: 1
Joined: Thu Nov 17, 2016 10:16 am

SNP data for polyploids

Postby mghanbari » Thu Nov 17, 2016 5:57 pm

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,

lckarssen
Site Admin
Site Admin
Posts: 321
Joined: Tue Jan 04, 2011 3:04 pm
Location: Utrecht, The Netherlands

Re: SNP data for polyploids

Postby lckarssen » Wed Nov 23, 2016 12:02 pm

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.
-------
Lennart Karssen
PolyOmica
The Netherlands
-------

Ritchie
Posts: 1
Joined: Mon Dec 12, 2016 8:15 am
Contact:

Re: SNP data for polyploids

Postby Ritchie » Tue Dec 13, 2016 7:11 am

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.

lckarssen
Site Admin
Site Admin
Posts: 321
Joined: Tue Jan 04, 2011 3:04 pm
Location: Utrecht, The Netherlands

Re: SNP data for polyploids

Postby lckarssen » Tue Dec 13, 2016 8:26 am

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.
-------
Lennart Karssen
PolyOmica
The Netherlands
-------


Return to “GenABEL”

Who is online

Users browsing this forum: Bing [Bot] and 2 guests