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Add an MN:i tag (number of SEQ bases at time of modification tag update). #714

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Sep 9, 2024
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Add an MN:i tag (number of SEQ bases at time of modification tag update). #714

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16 changes: 16 additions & 0 deletions SAMtags.tex
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Expand Up @@ -96,6 +96,7 @@ \section{Standard tags}
{\tt MI} & Z & Molecular identifier; a string that uniquely identifies the molecule from which the record was derived \\
{\tt ML} & B,C & Base modification probabilities \\
{\tt MM} & Z & Base modifications / methylation \\
{\tt MN} & i & Length of sequence at the time {\tt MM} and {\tt ML} were produced \\
{\tt MQ} & i & Mapping quality of the mate/next segment \\
{\tt NH} & i & Number of reported alignments that contain the query in the current record \\
{\tt NM} & i & Edit distance to the reference \\
Expand Down Expand Up @@ -625,6 +626,17 @@ \subsection{Base modifications}
{\tt ML} values for ambiguity codes give the probability that the modification is one of the possible codes compatible with that ambiguity code.
For example {\tt MM:Z:C+C,10; ML:B:C,229} indicates a C call with a probability of 90\% of having some form of unspecified modification.

\item[MN:i:\tagvalue{length}]
\hfill\\
The length of the {\sf SEQ} field at the time the {\tt MM} value was last written.

Some processing of aligned data, such as the use of hard-clipping tools, may alter {\sf SEQ} sequence data.
If the sequence is shortened in this manner then the base offsets in {\tt MM} and {\tt ML} become invalid unless they are also updated accordingly.

Some hard-clipping tools will update {\tt MM}/{\tt ML} but others do not, so the {\tt MN} tag offers a simple sanity check.
Software that wishes to validate {\tt MM} should compare the length of the {\sf SEQ} field with the contents of the {\tt MN} tag---if they differ, the {\tt MM}~and {\tt ML}~values should be considered out-of-date.
The tag is optional, but recommended, and if it is absent then there is an implicit assumption that the {\tt MM} data is valid unless evidence implies otherwise (e.g., by having coordinates beyond the end of the sequence).

\end{description}

\section{Draft tags}
Expand Down Expand Up @@ -671,6 +683,10 @@ \section{Tag History}
\setlength{\parindent}{0pt}
\newcommand*{\gap}{\vspace*{2ex}}

\subsubsection*{September 2024}

Added the MN tag for validating base modification tag consistency.

\subsubsection*{February 2022}

Base modification tags changed to use the predefined standard names MM and~ML, as their review period has finished.
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