cnvkit , antitarget , cn , call cnv

Question

[nina.naitatmane]

hello, Im using CNVkit on amplicon sequencing with ion torrent. we don't have normal samples. and antitargets are not really helpfull in our situation, i have big insertion and no deletion in results . Is cnvkit still usefull? Can we use cnvkit without antitarget ?

call command gives as a new element cn , what does it represent in real ? and why do I have cn cn1 cn2 in my results ? thank you so much for your help

Answer 1

[Eric T.]

1. Yes, you can use CNVkit with targeted amplicon sequencing data: http://cnvkit.readthedocs.io/en/stable/nonhybrid.html#targeted-amplicon-sequencing-tas
2. The cn column is the estimated absolute copy number, assuming diploid cells. The cn1 and cn2 columns are allele-specific copy number, assuming you've provided a VCF file. Details: http://cnvkit.readthedocs.io/en/stable/pipeline.html#call

[nina.naitatmane]

thank you, this helped me. how can interpret results, biologists on my lab are looking only for MET gen and its CNV ? thank you again

[Eric T.]

To clarify: CNVkit will work properly on targeted gene panels of at least 5 genes or so. If you're only sequencing one gene, the total copy number information will always be neutral (log2 = 0) because of normalization. But you can still look at b-allele frequency (the baf column in call output) to detect allelic imbalance, which would indicate a copy number alteration. Typically a lab would use FISH to determine a single gene's copy number.