estimate tumor purity from capture panel data using tumor-only mode

Question

[lffu_0032]

Hi, everyone, i have a question: i want to call CNV from FFPE tumor using capture panel data, I need to estimate the tumor purity to adjust the copy number, i only have tumor-only data, is there any public tools or method to do this job? many thanks here.

[German.M.Demidov]

For the reliable estimation of purity you need to be able to distinguish between germline and somatic event. I am afraid with tumor data only it is not really possible. It is kinda possible if you have purity much lower than 100%, but if it is close - no way, only if you say additionally "long copy-number change must be somatic", which is not necessarily true and you may have no long copy-number alterations in your data.

Answer 1

[markus.riester]

If you have at least a few processed-matched normals, you can try https://github.com/lima1/PureCN (disclaimer: our tool).