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NovembreLab / feems

MIT License
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input file other than plink files ? #8

Open anne-laureferchaud opened 3 years ago

anne-laureferchaud commented 3 years ago

Hi,

Thanks for developing such an interesting tool, that could make the difference in the application of conservation genetics ! I wish I will be available to run feems on my dataset. Could you please tell me if I can feed other inputs than plink file ? I have a dataset based on low coverage WGS, for which I have used the ANGSD pipeline in order to get Genotype Likelihoods (GL). Due to low coverage (1.3X) I cannot really call my genotypes but I am rather stocked with GL. So would it be possible to use an allele frequency matrix from those GL data or even a beagle file instead a plink file ?

Best, Anne-Laure

VivaswatS commented 1 year ago

Hi @anne-laureferchaud, sorry for the delayed response. We do not have functionality to incorporate uncertainty in the genotypes straight out of the box.

Ultimately, the method needs an allele frequency matrix that is # of demes x SNPs in size, so if you think you can create this with ANGSD then we can chat further. If you are interested in pursuing this avenue, you can email me at vivaswat@uchicago.edu.