Pre-processing query

[seedgeorge]

Hi,
I have multi-sample mutation data (mutect2) and also copy number data (battenberg). I'm happy creating the input files with allele counts, but was wondering about best practices for battenberg, as it reports both clonal and sub-clonal entries for CNAs?
Kind regards,
George

[aroth85]

Best bet it to use the clonal CNA calls. In principle these should be more common and account for more of the signal.

[seedgeorge]

Great, thanks. So I'll exclude mutations that overlap with areas of sub-clonal CNAs. In the future it'd be nice to model them in a more integrative manner...