Tool for CNV benchmarking vs gold standards

Question

[eric54321g]

Is there a tool (analogous to Truvari for SVs) that can be used for CNV accuracy assessment, given some gold standard samples. It should ideally output precision and recall for different CNV types and size ranges.

[WouterDeCoster]

Does Truvari not do the job here?

[eric54321g]

I read through the Truvari docs, and CNV isn't mentioned. Do you know if it can handle numeric gains and losses in some manner?

[WouterDeCoster]

Please use ADD COMMENT or ADD REPLY to answer to previous reactions, as such this thread remains logically structured and easy to follow. I have now moved your reaction but as you can see it's not optimal. Adding an answer should only be used for providing a solution to the question asked.

Isn't a CNV an SV then?

Answer 1

[German.M.Demidov]

https://github.com/TranslationalBioinformaticsIGTP/CNVbenchmarkeR ? However I have to say "detect a CNV" may mean many different things - for SVs breakpoints are usually considered ± inside an insert distance confidence intervals, for CNVs, expecially for targeted sequencing, it may mean detect CNs of regions. Again, except finding a site of CNVs, you may be interested in accuracy of genotyping.