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It is possible to run the tool CollectDuplexSeqmetrics on a consensus BAM file but the results will not be intuitively correct since metrics collection is expecting the input be raw reads (and not consensus sequences) annotated with the MI tag:
|1. The exact BAM output by the `GroupReadsByUmi` tool (in the sort-order it was produced in)
|2. A BAM file that has MI tags present on all reads (usually set by `GroupReadsByUmi` and has
| been sorted with `SortBam` into `TemplateCoordinate` order.
We should either support gathering metrics over the consensus BAM or raise an exception for unsupported behavior if any of the consensus SAM tags are encountered.
The text was updated successfully, but these errors were encountered:
It is possible to run the tool
CollectDuplexSeqmetrics
on a consensus BAM file but the results will not be intuitively correct since metrics collection is expecting the input be raw reads (and not consensus sequences) annotated with theMI
tag:fgbio/src/main/scala/com/fulcrumgenomics/umi/CollectDuplexSeqMetrics.scala
Lines 223 to 225 in d5b38ca
We should either support gathering metrics over the consensus BAM or raise an exception for unsupported behavior if any of the consensus SAM tags are encountered.
The text was updated successfully, but these errors were encountered: