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dcgerard / updog

Flexible Genotyping of Polyploids using Next Generation Sequencing Data
https://dcgerard.github.io/updog/
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Question about Model selection #13

Closed xuzhougeng closed 3 years ago

xuzhougeng commented 3 years ago

Hi, I've been using updog to genotype GBS data for a F2 population with 228 individual. I cross two homozygous diploid plant (P1 and P2) to get the F1 plant, and generate the F2 population by selfing. The parents (P1, P2) and 228 individual plant was sequenced by GBS technology.

When I read the help document of updog, I didn't find a model for F2 population but a S1 model. After I google the difference between F2 and S1, I get the following answer about F2 and S1.

however, with an f2 you usually don't know exactly how similar those 2 parents were genetically, while with s1 you know the parent was exactly the same. https://www.autoflower.net/forums/threads/s1-vs-f2.68858/

So, is it fine for me to use s1 for this experiment?

dcgerard commented 3 years ago

Hey @xuzhougeng, thanks for trying out updog!

An S1 population results from one generation of selfing. Since your F2 population results from selfing one individual, you should be able to use model = "s1" here.

For more general F2 populations (resulting from using multiple F1 individuals as parents), updog does not specifically support such genotype distributions of F2 populations, but you would still be able to use model = "norm" here since this genotype distribution is designed to be flexible enough to fit many genotype distributions.

xuzhougeng commented 3 years ago

Thanks for your kindly help!