Question: CNV detection techniques, algorithms, applications ...
0
gravatar for nina.naitatmane
5 weeks ago by
nina.naitatmane10 wrote:

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

ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by nina.naitatmane10
2

a useful website that references ngs tools :

https://omictools.com/cnv-detection3-category

ADD REPLYlink written 5 weeks ago by guillaume.rbt240

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

ADD REPLYlink written 5 weeks ago by Titus280

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

ADD REPLYlink written 5 weeks ago by nina.naitatmane10

I think the figure 1 is really clear about the strategies , what did you not understand ?

ADD REPLYlink written 5 weeks ago by Titus280
1
gravatar for andrew.j.skelton73
5 weeks ago by
Newcastle Upon Tyne
andrew.j.skelton733.1k wrote:

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

ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by andrew.j.skelton733.1k
1

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.

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by igor4.2k
1
gravatar for Corentin
5 weeks ago by
Corentin20
Corentin20 wrote:

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 ...).

ADD COMMENTlink written 5 weeks ago by Corentin20
0
gravatar for nina.naitatmane
5 weeks ago by
nina.naitatmane10 wrote:

Oh, Thanks a lot for your help :)

ADD COMMENTlink written 5 weeks ago by nina.naitatmane10
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