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The tumor DH panel makes me believe that either your tumor or your normal chip data is bad, or alternatively that the tumor and normal are not matched.
Check the allele B fraction of your normal. It should show three distinct bands. Do the same for the tumor. It should also show distinct bands with varying of bands depending on aberrations. If both look clean, then it's likely they're not matched. If one is very noisy, then that one is simply a bad run/sample.
Henrik
Two more questions that I haven't been able to find in the documentation..1- Is there a way to remove (or ideally prevent) very small segments? I'm finding several small (2-10 probes) segments with very high copy number (>10). I'm doubtful that they are all real.
2- I am finding very few deletions (<5 per genome, vs dozens of amplifications) in my samples. I'm calling gains/dels based on the standard deviation of the median probe log-ratio. Is this skewed distribution a common phenomena and should my threshold for deletions be more lenient than my threshold for gains?