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[SQUASH ME] Replace phred-true-scale language.
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jkbonfield committed Aug 19, 2021
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2 changes: 1 addition & 1 deletion VCFv4.3.tex
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Expand Up @@ -544,7 +544,7 @@ \subsection{VCF tag naming conventions}
\begin{itemize}
\item The `L' suffix means \emph{likelihood} as log-likelihood in the sampling distribution, $\log_{10} \Pr(\mathrm{Data}|\mathrm{Model})$.
Likelihoods are represented as $\log_{10}$ scale, thus they are negative numbers (e.g.\ GL, CNL).
The likelihood can be also represented in some cases as a phred-true scale ($-10 \log_{10}(probability\_of\_being\_correct)$) in a separate tag (e.g.\ PL).
In some cases the likelihood may also represented using a positive value in a separate tag (e.g.\ PL) using the $-10 \log_{10}(probability\_of\_being\_correct)$ scale.
In this case they may be normalised so the most likely event has a score of 0.
\item The `P' suffix means \emph{probability} as linear-scale probability in the posterior distribution, which is $\Pr(\mathrm{Model}|\mathrm{Data})$. Examples are GP, CNP.
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