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

broadinstitute / warp

WDL Analysis Research Pipelines

https://broadinstitute.github.io/warp

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Can't calculate duplicates from flag in BAM output of Optimus, Multiome, and Slideseq #1115

Open ekiernan opened 1 year ago

ekiernan commented 1 year ago

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 commented 12 months ago

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 commented 1 month ago

This is still an issue