Hello I have been following tutorial(s) 11682 and 11683 for sensitive detection of copy ratio alterations in benign tissue. Previously we have used other tools, such as Mutect2, to look at CNV when we had matched normal germline samples. Now however we would like to use a panel of normals, consisting of 47 samples, outlined in the tutorial without matched normals to look for copy ratio alterations in our benign case samples.
I have run several case samples through the tutorial and noticed that after running ModelSegments command some of the sample plots looked similar to those seen in figure 8D of the tutorial while others had many more segments and more noisy. I am not sure if this has to do with the denoising steps or the ModelSegments step? Any ideas and suggestions to address the discrepancy would be a great help! Thank you
Please sign in to leave a comment.