How to only mark duplicates without removing them?

[Dries-B]

For my workflow, I want to combine all information, including duplicates, into one BAM file. I am looking for similar behaviour to Picard's MarkDuplicates.

I was hoping --annotated_output_bam would give the desired output, but it does not contain the duplicate flag 1024. This file does contain tags though; could these be used for subsequent filtering?

[cgates]

Hi @Dries-B

Thanks for you interest in Connor. Takara Bio is the primary support for Connor and I've forwarded your question to them.

For my own part, I believe I understand your question and while Connor does not set the duplicate bit in the SAM flag, the annotated BAM file contains an undocumented tag, X6, which indicates that specific alignment would be the template for the consensus alignment sequence. So the absence of the X6 tag is roughly analogous to the duplicate SAM flag bit. I hope that helps.

Best,
cg