As noted in [documentation](https://gatk.broadinstitute.org/hc/en-us/articles/13832682540699-MarkDuplicatesSpark#:~:text=.%20It%20is%20recommended%20to%20subsequently%20run%20SetNmMdAndUqTags%20before%20running%20BQSR.) and previous [comment](https://github.com/uclahs-cds/pipeline-align-DNA/pull/138#discussion_r716233208)
