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Add succinct description of refget sequence collection in metadata #832

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8 changes: 8 additions & 0 deletions VCFv4.5.tex
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Expand Up @@ -357,6 +357,14 @@ \subsubsection{Pedigree field format}
\noindent See \ref{PedigreeInDetail} for details.


\subsubsection{Sequence collection format}
The reference sequences can be recorded as a sequence collection identifier\footnote{\url{https://ga4gh.github.io/refget/seqcols/}}
\begin{verbatim}
##seqcol=<ID=ga4gh:SC.hsgd70lp87g2u8sgsnd0g2fxxc,url=ga4gh_resolver_url>
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@tcezard tcezard Jun 25, 2025 •
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Using the non-structured format

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##seqcol=<ID=ga4gh:SC.hsgd70lp87g2u8sgsnd0g2fxxc,url=ga4gh_resolver_url>
##seqcol=ga4gh:SC.hsgd70lp87g2u8sgsnd0g2fxxc

\end{verbatim}
The ID section should contain the sequence collection identifier of the reference sequence that was used to generate the VCF prefixed with ga4gh:SC.
Only one refget-seqcol entry can be added per VCF.

\subsection{Header line syntax}
\label{header-line}
The mandatory header line names the 8 fixed, mandatory columns. These columns are as follows:
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