Introduced symbolic allele "<*>" in gVCF

VCFv4.3.tex

@@ -1057,22 +1057,21 @@ \subsection{Representing unspecified alleles and REF-only blocks (gVCF)}
 using the END INFO tag, an idea originally introduced by the gVCF file format\footnote{\url{https://support.basespace.illumina.com/knowledgebase/articles/147078-gvcf-file}}.
 The convention adopted here is to represent reference evidence as likelihoods against an
 unknown alternate allele. Think of this as the likelihood for reference as compared to any other possible alternate
-allele (both SNP, indel, or otherwise). A symbolic alternate allele ($<$X$>$ in
-samtools and $<$NON\_REF$>$ in GATK implementation) is used to represent this
-unspecified alternate allele.
+allele (both SNP, indel, or otherwise). A symbolic alternate allele $<$*$>$
+is used to represent this unspecified alternate allele.
 
 Example records are given below:
 \scriptsize
 \begin{flushleft}
 \begin{tabular}{ l l l l l l l l l l }
 \#CHROM & POS & ID & REF & ALT & QUAL & FILTER & INFO & FORMAT & Sample \\
-1 & 4370 & . & G & $<$X$>$ & . & . & END=4383 & GT:DP:GQ:MIN\_DP:PL & 0/0:25:60:23:0,60,900 \\
-1 & 4384 & . & C & $<$X$>$ & . & . & END=4388 & GT:DP:GQ:MIN\_DP:PL & 0/0:25:45:25:0,42,630 \\
-1 & 4389 & . & T & TC,$<$X$>$ & 213.73 & . & . & GT:DP:GQ:PL & 0/1:23:99:51,0,36,93,92,86 \\
-1 & 4390 & . & C & $<$X$>$ & . & . & END=4390 & GT:DP:GQ:MIN\_DP:PL & 0/0:26:0:26:0,0,315 \\
-1 & 4391 & . & C & $<$X$>$ & . & . & END=4395 & GT:DP:GQ:MIN\_DP:PL & 0/0:27:63:27:0,63,945 \\
-1 & 4396 & . & G & C,$<$X$>$ & 0 & . & . & GT:DP:GQ:P & 0/0:24:52:0,52,95,66,95,97 \\
-1 & 4397 & . & T & $<$X$>$ & . & . & END=4416 & GT:DP:GQ:MIN\_DP:PL & 0/0:22:14:22:0,15,593 \\
+1 & 4370 & . & G & $<$*$>$ & . & . & END=4383 & GT:DP:GQ:MIN\_DP:PL & 0/0:25:60:23:0,60,900 \\
+1 & 4384 & . & C & $<$*$>$ & . & . & END=4388 & GT:DP:GQ:MIN\_DP:PL & 0/0:25:45:25:0,42,630 \\
+1 & 4389 & . & T & TC,$<$*$>$ & 213.73 & . & . & GT:DP:GQ:PL & 0/1:23:99:51,0,36,93,92,86 \\
+1 & 4390 & . & C & $<$*$>$ & . & . & END=4390 & GT:DP:GQ:MIN\_DP:PL & 0/0:26:0:26:0,0,315 \\
+1 & 4391 & . & C & $<$*$>$ & . & . & END=4395 & GT:DP:GQ:MIN\_DP:PL & 0/0:27:63:27:0,63,945 \\
+1 & 4396 & . & G & C,$<$*$>$ & 0 & . & . & GT:DP:GQ:P & 0/0:24:52:0,52,95,66,95,97 \\
+1 & 4397 & . & T & $<$*$>$ & . & . & END=4416 & GT:DP:GQ:MIN\_DP:PL & 0/0:22:14:22:0,15,593 \\
 \end{tabular}
 \end{flushleft}
 \normalsize
@@ -1688,7 +1687,7 @@ \subsection{Changes between VCFv4.2 and VCFv4.3}
 \item In order for VCF and BCF to have the same expressive power, we state explicitly that Integers and Floats are 32-bit numbers. Integers are signed.
 \item We state explicitly that zero length strings are not allowed, this includes the CHROM and ID column, INFO IDs, FILTER IDs and FORMAT IDs. Meta-information lines can be in any order, with the exception of \#\#fileformat which must come first. INFO, FILTER and FORMAT IDs must be unique within that type.
 \item We state explicitly that duplicate IDs, FILTER, INFO or FORMAT keys are not valid.
-\item A section about gVCF was added
+\item A section about gVCF was added, introduced the $<$*$>$ symbolic allele.
 \item A section about tag naming conventions was added
 \end{itemize}