CNAs calling in tumor-normal WGS data
1
0
Entering edit mode
6 months ago

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.

CNA tumor-normal WGS • 316 views
ADD COMMENT
0
Entering edit mode

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 REPLY
0
Entering edit mode
6 months ago

Control-FREEC followed by PyClone.

ADD COMMENT
0
Entering edit mode

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 REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1479 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6