How to export CNVkit results into PyClone?

Question

[Jokhe]

Hi,

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!

[meizi2015]

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.

Answer 1

[Eric T.]

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.