“Remove PCR duplicates” is done twice in ATAC-Seq tutorial

I am struggling to understand, why the "Filter Option: Remove PCR duplicates” in the Genrich tool is set to "Yes" after running the MarkDuplicates tool with “If true do not write duplicates to the output file instead of writing them with appropriate flags set” set to "Yes". The list of PCR duplicates produced by Genrich is empty.

When I run Genrich with "Filter Option: Remove PCR duplicates” set to "No", I get the same result for the bedgraph pile up and the encode peak files.

Also, when I skip the MarkDuplicates step and run Genrich with "Filter Option: Remove PCR duplicates” set to "Yes", I get the same result. And this time with a list of 3549 PCR duplicates

Review the ATAC-Seq tutorial's MarkDuplicates and Genrich steps, focusing on the two PCR-duplicate filtering options described in the issue. Compare the outputs from the reported workflows and clarify the intended sequence or settings; done means the tutorial no longer presents redundant or misleading duplicate removal instructions.

Written by the indexing model from the issue text.