Hi! We've used CNVkit fairly extensively and are quite happy with it, thanks. We have rat tumor/normal WGS samples now, and CNVkit generates many, many small (~20kb) segments that oscillate between copy number 0 and copy number -0.5. The confidence intervals do not overlap each other and for the segments around -0.5 the ci do not overlap zero. The coverage is good, alignments were good, and nothing else seems odd about these samples, but this output is pretty strange. Any suggestions? Thanks!
You can post the figure generated by CNVKit.
I haven't tried posting pictures before so apologies if this didn't work! but here's a shot of the scatter plot.
1) Are the tumor and normal samples from the same rat? Or just from the same strain? There can be more heterogeneity than you expect sometimes.
I'm still not sure whether that would explain that result, though...
They're from the same rat.
Interestingly, we just ran Control-FREEC on the same data and got a small handful of discrete called CNVs, everything else normal ploidy.