Question: CNAs calling in tumor-normal WGS data
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gravatar for German.M.Demidov
4 weeks ago by
Tübingen
German.M.Demidov1.9k wrote:

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.

wgs tumor-normal cna • 133 views
ADD COMMENTlink modified 4 weeks ago by Kevin Blighe67k • written 4 weeks ago by German.M.Demidov1.9k

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)

ADD REPLYlink written 4 weeks ago by German.M.Demidov1.9k
0
gravatar for Kevin Blighe
4 weeks ago by
Kevin Blighe67k
Republic of Ireland
Kevin Blighe67k wrote:

Control-FREEC followed by PyClone.

ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by Kevin Blighe67k

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

ADD REPLYlink written 4 weeks ago by RamRS30k

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

ADD REPLYlink written 4 weeks ago by German.M.Demidov1.9k
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