I am trying to use CNVkit (https://cnvkit.readthedocs.io/en/stable/pipeline.html) to detect somatic copy number variations for 40 paired tumor-normal WES samples. I am able to run the pipeline based on the current documentation, but I am unsure how to determine based on the output, if the detected variants are germline or somatic. I am interested in obtaining both, but I am more focused on somatic copy number variations.
Additionally, I would like to be able to tune the parameters (I am using only the defaults now), to run the pipeline most effectively. For example, the autobin step, which bam files should be used, normal or tumor or both; or the reference, to continue to pool all normal or keep tumor-normal pairs for better somatic cnv detection.
Please let me know if you know of any advice or suggestions of how to proceed with this type of analysis. Thanks so much in advance!
Best Regards, Stephanie