Hello everyone, I'm a computer science student. For my intership, I have to implement a solution to detect CNV in NGS data, in a Cancer Institute. It's new domain for me, any help to understand existant methods and solutions, algotithms used, tutoriels ... Any help is welcome (in french or in english) . Thank you
If you're looking for somatic copy number events in exome data, check out GATK's best practises
Edit: I just noticed that GATK basically refer you to the workshop docs in that link (Super helpful, I know). In any case, here's the relevant doc
There are already a few tools out there for CNV detection: https://omictools.com/cnv-detection2-category . They are often specialised in Exome sequence data.
You can take a look at how they work. Their implementation is described in the associated paper (when there is one).
I know that some of them use a Hidden Markov Model to detect the CNVs (XHMM, Canoes, Condex ...).