What should the criteria (alpha) for discarding segregation distorted markers (SNP) be?

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Hong-yan Ren

Don't know what exact alpha do you mean in this context, however, when using admixture model in STRUCTURE, default value for alpha (Dirichlet Parameter for Degree of Admixture) is 1.0.

Brandon Joseph Schlautman

Are you doing linkage mapping with your GBS SNP markers? Significant marker distortion is common. If so you should attempt to create your linkage map first without markers with significant distortion (p