WebOct 18, 2024 · Output annotations. The Genotype Refinement workflow adds several new info- and format-level annotations to each variant. GQ fields will be updated, and genotypes calculated to be highly likely to be incorrect will be changed. The Phred-scaled genotype likelihoods (PLs) carry through the pipeline without being changed. WebPhred is actually the name of a program that was developed to maps the quality scores to ASCII characters. The method in more detail is explained in the original publication (which I admit had only went through): Ewing B, Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 1998 Mar;8 (3):186-94.
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