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In which step exactly the allele depth / frequency is used during variant calling?
I was thinking of how allele depth / frequency affect variant calling. I know that the HC is using Bayes to call variant. The question is how is allele depth / frequency information used during the variant calling?
Based on Bayes: The most possible variant allele is: P(G|D) = arg max P(G) * P(D|G). I initial thought that P(D|G) is the allele frequency of data. But feel something is not right.
Could you please share some comment? Thanks