Duplicates

[ghost]

Hello all,

I am trying to switch from the GATK best practices pipeline to the DRAGEN-GATK pipeline at the moment and ran into some confusion:
When doing the alignment with bwa mem, I detect 17329 duplicates with gatk MarkDuplicates after sorting, and compression.
When using dragmap V1.2.1 for the alignment, and keeping all other steps the same, I only detect 200 duplicates.

I got the data from a course, so I know the duplicate number of the alignment with bwa mem should be correct.
Both, bwa mem and dragmap were run in default settings.

Does anyone have an idea what could be the issue here?