feat: add tags related to optical duplicates.#813
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Picard has long been able to add Sam Tags that provide information about duplicate templates: Their type (Library or Sequencing), the size of the sets they are part of, and the queryname of the representative template within the set that is _not_ a duplicate. As I look to use these tags in another repository (fgbio) I wanted to make sure that the tags are generally accepted and well defined.
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I guess these are the tags that are described in MarkDuplicates.java: This does seem like a worthwhile addition, not least because the Git history suggests they've been in Picard for 8 or 10 years. DI and DT would need entries in §1.1 too, and they and the DS entry would want to explain what this is about a bit more. |
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I wasn't sure if the 1.1 section was required for all tags or only for those for which there's something interesting to say....but OK... :-) |
jmarshall
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Feb 17, 2025
| Use SQ if the duplication occurred during sequencing (e.g., due to imaging error, aka "optical duplicates", or due to | ||
| over-aggressive bridge-amp). | ||
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| \item[GL:f:\tagvalue{score}] |
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What is GL? Was this line accidentally committed?
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feat: add tags related to optical duplicates.
Picard has long been able to add Sam Tags that provide information about duplicate templates: their type (Library or Sequencing), the size of the sets they belong to, and the query name of the representative template within the set that is not a duplicate. As I look to use these tags in another repository (fgbio), I want to ensure they are generally accepted and well-defined.