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!
How did you run CNVkit? It looks as if it was run with two separate coverage profiles (genic and intergenic?) that were not normalized to each other when combining, so half the bins have log2 values shifted downward by 0.5. This could have happened if you ran
batch with WGS data but did not use
-m wgs, for example.