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which is the model i should use for GS using SNP effects

Hello everyone

I have a dataset of 300 eucalypts trees and 12K of bilallelic SNP where the Manhattan plot shows heterogeneous distribution for the marker effects. I fitted a BLUP model using GS3 program and r with phenotypes was higher than fitting a Bayesian model. How can I decide which model is the aproppiate? thanks for any help.

snp markers genomic selection blup bayes
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updated by Kevin Blighe Kevin Blighe • written by Jaime Zapata • Jaime Zapata

1 answer

Perform >3x cross validation on the models and check the CV error. The one with the smallest error is possibly the better model.

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written by Kevin Blighe Kevin Blighe

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