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Clarify Number=G tags in INFO as discussed in #272 #309

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12 changes: 11 additions & 1 deletion VCFv4.3.tex
Original file line number Diff line number Diff line change
Expand Up @@ -162,7 +162,17 @@ \subsubsection{Information field format}
\begin{itemize}
\item A: The field has one value per alternate allele. The values must be in the same order as listed in the ALT column (described in section \ref{data-lines}).
\item R: The field has one value for each possible allele, including the reference. The order of the values must be the reference allele first, then the alternate alleles as listed in the ALT column.
\item G: The field has one value for each possible genotype. The values must be in the same order as prescribed in section \ref{genotype-fields:genotype-ordering} (see \textsc{Genotype Ordering}).
\item G: The field has one value for each possible genotype.
Note that INFO tags declared as Number=G can have different number
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Should this block be reformatted to match the new 1 sentence per line formatting?

of values at each data line depending on the number of alleles and
the ploidy it represents and does not have to correspond to the
ploidy of samples in FORMAT fields. For example, with one alternate
allele, the tag can have two values (corresponding to the two
possible haploid genotypes R,A); three values (corresponding to the
three possible diploid genotypes RR, RA, AA); etc. The values must
be in the same order as prescribed in section
\ref{genotype-fields:genotype-ordering} (see \textsc{Genotype
Ordering}).
\item . (dot): The number of possible values varies, is unknown or unbounded.
\end{itemize}

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