For the next release (so NOT 3.9.0) I already have something on the way (its an improvement to the varlociraptor implementation): https://github.com/nf-core/sarek/pull/2208 but for the tests to pass I need to update bcftools which I started in https://github.com/nf-core/sarek/pull/2210 if anyone wants to continue with the bcftools update (I am sure there are some things that need fixing) that would be great 🙂