Hi, I have some sequencing files which include 8nt molecular indexes on both ends. So I remove them before mapping to the genome, and now I would like to deduplicate the reads with same molecular indexes. I found https://github.com/mbusby/AddUMIsToBam but not sure it is maintained and properly tested (and could not compile as, I think, some header files are missing) which theoretically would be good option when followed by a picard deduplicate step.
Would you have any experience or suggestion for this?
Thanks, Manu