Hi @bilgehannevruz, thanks for the feedback!
The ancestor of covtobed (called 'coverage'), did this, but it's old and the source is not available for licensing issues. The binary ships with the docker image and can be used like

coverage -i panel_02.bam -t target_regions.bed --bed > output.bed

Having this said, it's in our wish list to provide this functionality, but it won't happen in the immediate future, unfortunately.

We are testing a new version with bed support, but release is not imminent.

For the records I drafted a Python script to merge a GTF (or BED) and a covtobed-output (BED) here:
https://gist.github.com/telatin/82b4c51b7085dd0597659de0cf632d2a

@telatin

Thank you for the information and provided gist.

Quick update:
there is a "covtotarget" tool that can be applied downstream.

Info:
https://github.com/telatin/covtools/blob/master/README.md#covtotarget

Linux binary:
https://github.com/telatin/covtools/tree/master/release