extract polymorphic sites from genlight

[Marcelo Rosas]

Dear dartR team & friends

I have a genlight object obtained from Diversity Arrays Technology (DArT), with 92 genotypes 143,596 binary SNPs, size 126.7Mb 

and I want to extract the polymorphic sites (one for each SNPs) from this genlight to reduce the size of the matrix for phylogenetic reconstruction.

Is there a direct method from genligth?

Regards

Marcelo

[Jose Luis Mijangos]

Hi Marcelo,

You can filtered out fragments with more than one SNP using the function gl.filter.secondaries() and filtered out monomorphic loci suing the function gl.filter.monomorphs()

I also recommend reading our filtering tutorial using the link below:

http://georges.biomatix.org/storage/app/media/uploaded-files/tutorial5dartrbasicfiltering22-dec-21-2.pdf

Cheers,

Luis

[Marcelo Rosas]

Hi Luis, thank you for your attention,

Hello Luis, thanks for your attention,

I have already filtered the monomorphic loci

thanks

Marcelo R