It is a chunky one: github.com/nf-core/sarek/stack/2419 Adding filtering and joint calling for parabricks haplotypecaller. same as for mutect2/mutectcaller this triggered a bit a of refactoring to allow repurposing of subworkflows, which I split out into a stacked PR for sentieon. During this I also found a bug where unfiltered vcfs are not annotated if filtering is skipped ( we had a similar bug in mutect2). Let me know what you think