Copy-Number Enhancements - Ascat joint calling

[maxulysse]

Description of feature

From @seedgeorge

Hi there.
I think Sarek is in a good place with the current ASCAT implementation, but I'd like to point towards two things that I think would be helpful for the community.

• A bigger request here, but one that I think is an obvious next step for the pipeline. Sarek currently supports multi-sample calling with Mutect2 (hooray!) and ASCAT also supports this feature, with the paper here and documentation here. It effectively uses both the logr and BAF tracks across all same-patient tumour samples to jointly find segments, helping a) breakpoint accuracy (particularly with smaller segments) and b) downstream interpretation of CNA data.

Kind regards,
George