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 is also more info with discussion about GATK CNV here: http://gatkforums.broadinstitute.org/gatk/discussion/6791/description-and-examples-of-the-steps-in-the-cnv-case-and-cnv-pon-creation-workflows
Keep in mind, this is for GATK 4, which is officially not ready yet.
Hi,
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 ...).
Oh, Thanks a lot for your help :)
Log in to answer this question.
a useful website that references ngs tools :
https://omictools.com/cnv-detection3-category
Hi , May be you already see this paper but it really helped me to understand the problematic around CNV : https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-S11-S1
Thank you, it really helps, but I didn't understand the strategies :RD ,PEM, RC ..... If you have some article about that, I would be gratefull. Thank you
I think the figure 1 is really clear about the strategies , what did you not understand ?