pepr parameterisation: germline filtering (revert-revert)
pepr parameterisation: germline filtering (revert-revert)

Contrary to the previous revert of these setting changes, we now think
the changes outside the HC region can be ignored given the lack of
knowledge about truth. LowQual is left in place for now.

hartwigmedical/pipeline,hartwigmedical/pipeline,hartwigmedical/pipeline