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dariober / cnv_facets

Somatic copy variant caller (CNV) for next generation sequencing
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question about ploidy estimate #54

Closed guillaume-rs closed 1 year ago

guillaume-rs commented 1 year ago

Hi, I've used CNV_facets on multiple WES samples. For some of them I get a high estimated ploidy (around 4). To my understanding it can correspond to whole genome duplication event, or an error in the estimated ploidy and average diploid state. Here is an example of such results :

image

I'm not used to interpret CNV genomic profile and I'm not sure to what extend this result is relevant. Does it look like an obvious mistake from FACETS or could it be indeed due to a duplication event?

Many thanks, Guillaume

dariober commented 1 year ago

Hi Guillaume - I can't tell, really. I have to say that I haven't looked a CNVs for quite a while even if I'm happy to maintain the cnv_facets package. Try posting this on the FACETS repository where the developer(s) may have a better view. (Remember that cnv_facets is just a convenient wrapper around the FACETS R package)

guillaume-rs commented 1 year ago

Hi Dario, Thank you very much for your quick feedback. I will ask this on the FACETS repository.