Question: Tool for CNV benchmarking vs gold standards
0
gravatar for eric54321g
5 months ago by
eric54321g0
eric54321g0 wrote:

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.

cnv • 190 views
ADD COMMENTlink modified 3 months ago by Biostar ♦♦ 20 • written 5 months ago by eric54321g0

Does Truvari not do the job here?

ADD REPLYlink written 5 months ago by WouterDeCoster43k

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?

ADD REPLYlink written 5 months ago by eric54321g0

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?

ADD REPLYlink written 5 months ago by WouterDeCoster43k
1
gravatar for German.M.Demidov
3 months ago by
Tübingen
German.M.Demidov1.5k wrote:

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.

ADD COMMENTlink modified 3 months ago • written 3 months ago by German.M.Demidov1.5k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1117 users visited in the last hour