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Updated changelog to include all 4.5 changes
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d-cameron committed Apr 20, 2024
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Expand Up @@ -2647,10 +2647,15 @@ \section{List of changes}
\subsection{Changes between VCFv4.5 and VCFv4.4}
\begin{itemize}
\item Added DNA base modification support (FORMAT M5mC, M5hmC, M5fC, M5caC, M5hmU, M5fU, M4mC, M6mA, etc).
\item Reserved all FORMAT keys starting with M then a digit as base modification fields.
\item Added Number=P support for fields with cardinality matching sample ploidy/local copy number.
\item Added local allele support (Number=LA, LG, LR; FORMAT LAA, LAD, LADF, LADR, LEC, LGL, LGP, LGT, LPL, LPP) to reduce the size of multi-sample VCFs and enable lossless merging.
\item Deprecated INFO END. It is now a computed field written only for backwards compatibility with older versions of VCF.
\item Updated BCF rlen field to reflect INFO END being a computed value.
\item Added FORMAT LEN to support sample-specific $<$*$>$ alleles.
\item Clarified that the header line is indeed mandatory
\item Clarified that $<$NON\_REF$>$ should be treated as an alias of $<$*$>$
\end{itemize}
\subsection{Changes between VCFv4.4 and VCFv4.3}
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