CNAs calling in tumor-normal WGS data

Question

[German.M.Demidov]

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.

[German.M.Demidov]

Sorry guys for answering my own question -

https://github.com/hartwigmedical/hmftools/tree/master/purity-ploidy-estimator

I like this tool so far (not an advertisement, it is just well written with only minor problems for running and looks like it does the job)

Answer 1

[Kevin Blighe]

Control-FREEC followed by PyClone.

[Ram]

There is no need to sign off using your username in every answer, especially when the username is a play on the website name.

[German.M.Demidov]

Thank you! Yes, maybe I just should PyClone after calling...