Is your feature request related to a problem? Please describe.
Somatic SV calling (for WGS data) & purity/ploidy estimation have been neglected, it's time to give them some attention

Describe the solution you'd like

• Test current implementation of somatic SV calling with most recent manta version, add options to ignore unplaced, unlocalized, decoys, HLA, ... contigs, as well as optionally include user-defined configuration file.
• Test current ASCAT implementation for WGS, and compare it with manual runs. The wrappers need to be updated.