Question: cnvkit , antitarget , cn , call cnv
gravatar for nina.naitatmane
2.8 years ago by
nina.naitatmane20 wrote:

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

cnv • 1.1k views
ADD COMMENTlink modified 2.8 years ago by Eric T.2.6k • written 2.8 years ago by nina.naitatmane20
gravatar for Eric T.
2.8 years ago by
Eric T.2.6k
San Francisco, CA
Eric T.2.6k wrote:
  1. Yes, you can use CNVkit with targeted amplicon sequencing data:
  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:
ADD COMMENTlink written 2.8 years ago by Eric T.2.6k

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

ADD REPLYlink written 2.8 years ago by nina.naitatmane20

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.

ADD REPLYlink written 2.8 years ago by Eric T.2.6k
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