Question: normalization when calling CNV areas on a genome-wide scale in tumor-germline samples
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gravatar for Bogdan
4 weeks ago by
Bogdan480
Palo Alto, CA, USA
Bogdan480 wrote:

Dear all,

please would you advise : what is a more reliable method for normalization when calling CNV areas on a genome-wide scale on tumor-germline paired samples ?

And : shall we apply the normalization on a chromosome basis, or on a whole-genome ? Thanks a lot !

-- bogdan

cnv • 88 views
ADD COMMENTlink written 4 weeks ago by Bogdan480

I'd encourage you to use an existing package that rolls these normalizations in, rather than trying to reinvent the wheel. As a self-link, copyCat (https://github.com/chrisamiller/copyCat/) does mapability, GC correction, as well as normalizing global read depth. There are other tools that do similar things.

ADD REPLYlink written 4 weeks ago by Chris Miller19k

Dear Chris, thank you for your suggestions.

I would be very glad to use copyCat . A question though : I have seen distinct packages doing 1) global (genome-wide) normalization or 2) local (chromosome-wide) normalization ?

Would you recommend to use 1) or 2) or perhaps I shall use both normalization methods and compare the results ? Sometimes, on some tumor samples that we have, depending on how we do the normalization, we can call a region CN1 or CN3. Thanks !

ADD REPLYlink written 4 weeks ago by Bogdan480

If given samtools input, copy cat will exclude chromosomes from depth normalization that appear to differ substantially from CN2, based on allele frequency information. This information is more coarse than what you'd get from programs like ABSOLUTE or TITAN_CNA, that use allele frequency but is a quick way to do it that works reasonably well on most samples.

ADD REPLYlink written 4 weeks ago by Chris Miller19k

Thank you Chris for your gracious help ..

ADD REPLYlink written 4 weeks ago by Bogdan480
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