diff --git a/SAMtags.tex b/SAMtags.tex index eba269c7..197f9967 100644 --- a/SAMtags.tex +++ b/SAMtags.tex @@ -77,6 +77,9 @@ \section{Standard tags} {\tt CS} & Z & Color read sequence \\ {\tt CT} & Z & Complete read annotation tag, used for consensus annotation dummy features \\ {\tt CY} & Z & Phred quality of the cellular barcode sequence in the {\tt CR} tag \\ + {\tt DI} & Z & Duplicate Identity, for identifying the queryname that this read is a duplicate of\\ + {\tt DS} & i & Duplicate-set Size containing the size of the duplicate set\\ + {\tt DT} & Z & Duplicate type, used to identifying duplicate reads as coming from the library-construction (LB) or sequencing (SQ)\\ {\tt E2} & Z & The 2nd most likely base calls \\ {\tt FI} & i & The index of segment in the template \\ {\tt FS} & Z & Segment suffix \\ @@ -158,6 +161,21 @@ \subsection{Additional Template and Mapping data} \item[CP:i:\tagvalue{pos}] Leftmost coordinate of the next hit. +\item[DI:Z:\tagvalue{rname}] +(For duplicate templates) The queryname of the template that is not marked as duplicate +and that this template is a duplicate of. + +\item[DS:i:\tagvalue{count}] +Size of the duplicate set that the template is part of. + +\item[DT:Z:\tagvalue{str}] +(For duplicate templates) Either LB or SQ indicating the source of the duplication. +Use LB if the duplication occurred during library-construction (e.g., via PCR). +Use SQ if the duplication occurred during sequencing (e.g., due to imaging error, aka "optical duplicates", or due to +over-aggressive bridge-amp). + +\item[GL:f:\tagvalue{score}] + \item[E2:Z:\tagvalue{bases}] The 2nd most likely base calls. Same encoding and same length as {\sf SEQ}. See also {\tt U2} for associated quality values.