somatic variants in BAF plots

[molpatho]

Hi,

I have a question regarding the interpretation of BAF plots and the ML.somatic classification in PureCN.

In the PureCN publication and documentation, the BAF plots are described as representing predicted germline variants. However, when inspecting the xxx_variants.csv output, I noticed that variants with ML.somatic = TRUE are also included in the BAF plots.

BAF plots include variants that are later classified as somatic because the BAF modeling assumes most variants are germline before ML.somatic is inferred. Could you please confirm whether this interpretation is correct or not?

Thanks a lot.

Peony