fulcrumgenomics/fgbio

Warn or raise an exception when CollectDuplexSeqMetrics is run on a consensus BAM

clintval opened this issue · 0 comments

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.