We have some ChIP data with UMIs in the reads. We are planning to duplicate mark using either umi_tools or Picard to mark duplicates in a UMI aware fashion.
I see in the docs that MACS will mark duplicates in its own way: https://github.com/taoliu/MACS/wiki/Advanced%3A-Call-peaks-using-MACS2-subcommands
Ideally we could keep all the sequenced reads in the BAM files and have MACS use the duplicate status as it was set by our duplicate marking tool.
Has anyone tried this sort of thing? Perhaps my understand of how MACS works is incorrect?