Can't calculate duplicates from flag in BAM output of Optimus, Multiome, and Slideseq

[ekiernan]

The tool we use in for calculating optical/technical duplicate reads from the STARsolo BAMs requires a flag of 1024, which is captured in the BAM_FDUP attribute of the htslib.sam.h library used by TagSort. STARSolo does not currently output this for duplicate reads.

We can explore an alternative solution for duplicate calculations.

[ekiernan]

We are still exploring options for this. Documentation has been updated to reflect that the TagSort metric is not calculated for the Optimus workflow. https://broadinstitute.github.io/warp/docs/Pipelines/Optimus_Pipeline/Loom_schema

[jessicaway]

This is still an issue