Dear community members,
this question was discussed a lot here, but I could not find an answer that satisfied me fully =)
I need to call CNAs in tumor-normal WGS data (only 1 patient, 2 samples). I need to understand sub-clonal structure, purity and ploidy.
ASCAT - does not like sub-clonality (at least in my experience with arrays and ASCAT 1 year ago) - when it sees a subclonal event, it prefers to raise ploidy rather than to introduce a sub-clone.
Battenberg - I can not install. Just no way.
CANVAS - calls either tumor-only WGS or tumor-normal targeted seq.
ABSOLUTE - works with targeted seq mainly, requires quite time-consuming adaptation for WGS.
GATK - nice tool but requires a panel of normals.
What would you recommend? I am more aiming at the usability of the tool, not at the max accuracy. CNV-kit is great and usability is amazing but it is not very interpretable in the end + incorporation of BAF is far from full there, in my opinion.