Question: CNV details about the normal samples?
gravatar for kvn95ss
13 months ago by
kvn95ss0 wrote:

I'm using CNVkit to detect copy number changes in my samples which have been obtained from amplicon sequencing (sequenced region is around 330kb). I have 8 normal samples and 20 test samples. I can detect the copy number regions in the test samples, however how do I find out the copy number changes in the normal samples?

I created a reference CNN using the normals and reference genome (hg19). The CNN file generated does show the chr,start,end, log2, among other things. Can I use the log2 value to determine the copy number regions in the normal samples, or is there any other way to find out that information?

Any help appreciated!

cnv cnvkit • 407 views
ADD COMMENTlink modified 13 months ago by toralmanvar770 • written 13 months ago by kvn95ss0
gravatar for toralmanvar
13 months ago by
toralmanvar770 wrote:

This question has been beautifully answered in previous biostar post. Hope it will help.

ADD COMMENTlink written 13 months ago by toralmanvar770

Thanks for the info! That is sort of what I needed. Is there anyway to know the CNV in individual controls?

ADD REPLYlink written 13 months ago by kvn95ss0

Yes, you can run the rest of the pipeline with the control samples' targetcoverage.cnn and antitargetcoverage.cnn files versus the existing reference.cnn file, as if the controls were additional test samples. The rest of the pipeline is the same after you've run the fix command.

Or, if you don't mind some recomputation, run batch *_Normal.bam -r cnv-reference.cnn to reprocess the control samples from scratch using the reference you previously built.

In general CNVkit's segmented calls are larger than the common germline CNVs you see in healthy cells, so you shouldn't see much happening in the control samples.

ADD REPLYlink written 13 months ago by Eric T.2.5k
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