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etal / cnvkit

Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
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changing ploidy values do not change call outcomes #756

Open CKZan opened 2 years ago

CKZan commented 2 years ago

Running CNVkit call with default pramaters I got excessive loss call so I have tried using –ploidy 3 then –ploidy 4 and 5. I was expecting some changes on the results but they were the same. Would you help to explain what I have done wrong? The run command is cnvkit/0.9.1/cnvkit.py call xx.cns –ploidy 3 -o xx.call.cns

tetedange13 commented 2 years ago

Hi @CKZan ,

Are you really running CNVkit v0.9.1? => It is currently at v0.9.9, so please update and see if you still got this issue ?

Hope this helps ! Felix.

CKZan commented 2 years ago

Hi Felix, Yes I used cnvkit/0.9.9/cnvkit.py call and got the same results. For example by using default I got gain covered 100Mb and loss covered 150Mb then with ploidy 3,4 or 5 I got the same gain = 100Mb and loss = 150Mb where individual segment cn call did change like below

                chromosome  start             end          cn

Default 10 120052576 120140562 4 Ploidy =3 10 120052576 120140562 6 Default 11 60963220 60970805 5 Ploidy =3 11 60963220 60970805 8

These increace “cn” are only observed in gain regions.

From reading CNVkit document, log2 is scaled by given ploidy if ploidy is higher then shouldn’t I get lower copy number call?
I also used --center median but got more loss then gain. For the purpose of reducing loss call region without twisting -m threshold -t log2 value is there any parameter option that helps to reduce loss call?

Thank you for your help!

tetedange13 commented 2 years ago

Hi @CKZan,

Thanks for updating !

If I understand correctly :

  1. Your initial issue was that you got "excessive loss call" => What do you mean by that ? Could you share a scatterplot of your data ? => What type of input data do you have ? WGS ? Targetted ? If so, which enrichment method, hybrid-capture or amplicon ?

  2. Trying to tweak --ploidy param to reduce your number of loss calls, you noticed that higher ploidy value actually results in higher CN values in gain regions

Could you also share corresponding log2ratio value for both gained segments you showed ? ("chr10:120052576-120140562" and "chr11:60963220-60970805")

Thanks again ! Have a nice day, Felix.