Question: How to export CNVkit results into PyClone?
gravatar for Jokhe
3.0 years ago by
Jokhe110 wrote:


I have performed targeted amplicon sequencing for paired normal-tumor samples and recently identified both somatic mutations (VarScan2 somatic) and copynumber changes (CNVkit's batch command) in my samples. I would like to move on and study the tumour heterogeneity within my samples with PyClone.

Manual of CNVkit describes how data is exported into THetA2. However, as a beginner I find the manual little bit hard-to-read especially what comes to heterogeneity analysis and I can't figure out how I should run the program to obtain the input file for PyClone. Based on previous posts I know that some people have had good results with CNVkit+PyClone. I would like to see similar example script for the use with PyClone as well. Could anyone provide an example?

Thank you in advance!

pyclone cnvkit • 1.6k views
ADD COMMENTlink modified 3.0 years ago by Eric T.2.6k • written 3.0 years ago by Jokhe110

Hi Eric, i have the same question with you. I have download the WES data and used mutect2 to call somatic mutations and CNVkit to call CNV. But i really don't know how can i create the tsv file for pyclone. If you have solved this problem, please teach me how to do. Thank you.

ADD REPLYlink written 13 months ago by meizi201520
gravatar for Eric T.
3.0 years ago by
Eric T.2.6k
San Francisco, CA
Eric T.2.6k wrote:

I don't have a script for doing this, but if someone else has one I'd be happy to include it in the main CNVkit distribution. (Same goes for documentation.)

A good start might be to run export nexus-ogt to align b-allele frequencies to segments, then process or edit that output file further to format it for PyClone.

ADD COMMENTlink written 3.0 years ago by Eric T.2.6k
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