This image shows the log2 ratio of tumor coverage over control coverage for each exon capture region. As you can see there is a clear bias with GC content, making segmentation useless. Both samples are of good quality, sequenced using the same exon capture kit (but different sequencing batches) and there is unlikely to be contamination (as determined by mapping rate, which is near 100% to GRCm38). The control tissue is from liver.
Any suggestions on how I could try and correct the bias? I would expect log2 fold changes to have equal variance across GC content range.
I should also add that the CNV algorithms I've tried do correct for GC bias, but they were not sufficient.