Clarify the multiple incompatible uses of "phred-scale".

Sometimes this refers to $10 log_{10}(p)$, sometimes to $10
log_{10}(1-p)$, and sometimes to something normalised so $p$ isn't
really a probability at all.

Note CNL, CNP and CNQ don't mention phred anywhere in their
short description and only Phred in the long description for CNQ, so
I applied the same logic to PL, PP (is this correct?) and PQ.

Also clarified the "VCF tag naming conventions" part.  I changed
phred-scale in one part there to phred-true-scale.  I'm not so happy
with that, but as it's immediately followed by the formula I think
it's clear.

Author: jkbonfield

VCFv4.3.tex

@@ -427,9 +427,9 @@ \subsubsection{Genotype fields}
       GT		& 1		& String	& Genotype \\
       HQ		& 2		& Integer	& Haplotype quality \\
       MQ		& 1		& Integer	& RMS mapping quality \\
-      PL		& G		& Integer	& Phred-scaled genotype likelihoods rounded to the closest integer \\
-      PP		& G		& Integer	& Phred-scaled genotype posterior probabilities rounded to the closest integer \\
-      PQ		& 1		& Integer	& Phasing quality \\
+      PL		& G		& Integer	& $-10 log_{10}$ scaled genotype likelihoods rounded to the closest integer\\
+      PP		& G		& Integer	& $-10 log_{10}$ scaled genotype posterior probabilities rounded to the closest integer\\
+      PQ		& 1		& Integer	& Phred-scaled phasing quality\\
       PS		& 1		& Integer	& Phase set \\
 \end{longtable}
 
@@ -515,8 +515,8 @@ \subsubsection{Genotype fields}
 
   \item HQ (Integer): Haplotype qualities, two comma separated phred qualities.
   \item MQ (Integer): RMS mapping quality, similar to the version in the INFO field.
-  \item PL (Integer): The phred-scaled genotype likelihoods rounded to the closest integer, and otherwise defined in the same way as the GL field.
-  \item PP (Integer): The phred-scaled genotype posterior probabilities rounded to the closest integer, and otherwise defined in the same way as the GP field.
+  \item PL (Integer): The $log_{10}$ scaled genotype likelihoods rounded to the closest integer, and otherwise defined in the same way as the GL field.
+  \item PP (Integer): The $log_{10}$ scaled genotype posterior probabilities rounded to the closest integer, and otherwise defined in the same way as the GP field.
   \item PQ (Integer): Phasing quality, the phred-scaled probability that alleles are ordered incorrectly in a heterozygote (against all other members in the phase set).
   We note that we have not yet included the specific measure for precisely defining ``phasing quality''; our intention for now is simply to reserve the PQ tag for future use as a measure of phasing quality.
   \item PS (non-negative 32-bit Integer): Phase set, defined as a set of phased genotypes to which this genotype belongs.
@@ -544,13 +544,14 @@ \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 phred-scale in a separate tag (e.g.\ PL).
+    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 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.
 
     \item The `Q' suffix means \emph{quality} as log-complementary-phred-scale posterior probability, $-10 \log_{10} \Pr(\mathrm{Data}|\mathrm{Model})$, where the model is the most likely genotype that appears in the GT field.
     Examples are GQ, CNQ.
-    The fixed site-level QUAL field follows the same convention (represented as a phred-scaled number).
+    The fixed site-level QUAL field follows the same convention (represented as a phred-scaled number with $QUAL = -10 \log_{10}(probability\_of\_being\_incorrect)$).
 \end{itemize}
 
 
@@ -2085,6 +2086,7 @@ \section{List of changes}
 \subsection{Changes to VCFv4.3}
 
 \begin{itemize}
+\item Clarify distinction between Phred ($-10 log_{10}(p\_of\_incorrect)$) and $-10 log_{10}(p\_of\_correct)$.
 \item More strict language: ``should'' replaced with ``must'' where appropriate
 \item Tables with Type and Number definitions for INFO and FORMAT reserved keys