--annotations_filter should become a common filter option

[nvnieuwk]

Description of the bug

--annotations_filter should be reworked to a more common --output_filter that will run on the output VCFs of the pipeline instead of only on the annotated VCFs. This will make it easier to implement custom filters instead of relying on --annotate to be used.

Command used and terminal output

Relevant files

No response

System information

No response