[SQUASH ME]

Replace log with \log in updated text.

VCFv4.2.tex

@@ -223,7 +223,7 @@ \subsubsection{Genotype fields}
   \item FT : sample genotype filter indicating if this genotype was ``called'' (similar in concept to the FILTER field). Again, use PASS to indicate that all filters have been passed, a semicolon-separated list of codes for filters that fail, or `.' to indicate that filters have not been applied. These values should be described in the meta-information in the same way as FILTERs (String, no whitespace or semicolons permitted)
   \item GL : genotype likelihoods comprised of comma separated floating point $log_{10}$-scaled likelihoods for all possible genotypes given the set of alleles defined in the REF and ALT fields. In presence of the GT field the same ploidy is expected and the canonical order is used; without GT field, diploidy is assumed. If A is the allele in REF and B,C,... are the alleles as ordered in ALT, the ordering of genotypes for the likelihoods is given by: F(j/k) = (k*(k+1)/2)+j.  In other words, for biallelic sites the ordering is: AA,AB,BB; for triallelic sites the ordering is: AA,AB,BB,AC,BC,CC, etc.  For example: GT:GL 0/1:-323.03,-99.29,-802.53 (Floats)
   \item GLE : genotype likelihoods of heterogeneous ploidy, used in presence of uncertain copy number. For example: GLE=0:-75.22,1:-223.42,0/0:-323.03,1/0:-99.29,1/1:-802.53 (String)
-  \item PL : the $-10 log_{10}$ scaled genotype likelihoods rounded to the closest integer, and otherwise defined in the same way as the GL field (Integers).
+  \item PL : the $-10 \log_{10}$ scaled genotype likelihoods rounded to the closest integer, and otherwise defined in the same way as the GL field (Integers).
   \item GP : the phred-scaled genotype posterior probabilities (and otherwise defined precisely as the GL field); intended to store imputed genotype probabilities (Floats)
   \item GQ : conditional genotype quality, encoded as a phred quality $-10log_{10}$ p(genotype call is wrong, conditioned on the site's being variant) (Integer)
   \item HQ : haplotype qualities, two comma separated phred qualities (Integers)

VCFv4.3.tex

@@ -427,8 +427,8 @@ \subsubsection{Genotype fields}
       GT		& 1		& String	& Genotype \\
       HQ		& 2		& Integer	& Haplotype quality \\
       MQ		& 1		& Integer	& RMS mapping 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 \\
+      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 $-10 log_{10}$ scaled genotype likelihoods rounded to the closest integer, and otherwise defined in the same way as the GL field.
-  \item PP (Integer): The $-10 log_{10}$ scaled genotype posterior probabilities rounded to the closest integer, and otherwise defined in the same way as the GP field.
+  \item PL (Integer): The $-10 \log_{10}$-scaled genotype likelihoods rounded to the closest integer, and otherwise defined in the same way as the GL field.
+  \item PP (Integer): The $-10 \log_{10}$-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.
@@ -2086,7 +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 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
 

VCFv4.4.draft.tex

@@ -432,8 +432,8 @@ \subsubsection{Genotype fields}
       GT		& 1		& String	& Genotype \\
       HQ		& 2		& Integer	& Haplotype quality \\
       MQ		& 1		& Integer	& RMS mapping 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 \\
+      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}
@@ -520,8 +520,8 @@ \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 $-10 log_{10}$ scaled genotype likelihoods rounded to the closest integer, and otherwise defined in the same way as the GL field.
-  \item PP (Integer): The $-10 log_{10}$ scaled genotype posterior probabilities rounded to the closest integer, and otherwise defined in the same way as the GP field.
+  \item PL (Integer): The $-10\log_{10}$-scaled genotype likelihoods rounded to the closest integer, and otherwise defined in the same way as the GL field.
+  \item PP (Integer): The $-10\log_{10}$-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.
@@ -2224,7 +2224,7 @@ \subsection{Changes between VCFv4.4 and VCFv4.3}
 \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 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