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Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.
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question about ploidy estimate #193

Open guillaume-rs opened 1 year ago

guillaume-rs commented 1 year ago

Hi, I've used 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 indeed look like a duplication event or is there any hints of something going wrong?

Many thanks, Guillaume

veseshan commented 1 year ago

The high ploidy is likely due to chr15 having low allelic imbalance (logOR) while chr7q and chr9q have high logOR while at the same logR (total copy number state). Can't confidently claim that nothing is going wrong. What is the coverage depth? For a WES sample the points in the plots have more variability that I have seen.