I have vcf file where each plant line is represented by 3 technical replicates. To show that my replicates are consistent I did PC analysis and visualized the results by plotting PC1 vs PC2 and coloring the replicates of the lines. On a plot the replicates of the same line cluster closer than the replicates among different lines. However, this is just a graphical representation of replicate consistency. And I want to make a statistical test to demonstrate this inference in more formal way.

By analogy with the analysis of phenotype data by ANOVA I think that there should be a test similar to ANOVA which would infer the following model: genotype consistency (variance?) ~ line + replicate + line*replicate

I have no clear vision of how to **measure** the whole genotype consistency ar variance among replicates and genotypes as a trait.

So if such test exists, please, suggest how to use it having a vcf and line-replicate meta-data file as a input and/or suggest some other approach/method.