I am trying to run the analysis specified below:
http://cnvkit.readthedocs.io/en/stable/tumor.html under "Next steps"
For the careful: Run batch with just the normal samples specified as normal, yielding coverage .cnn files and a pooled reference. Inspect the coverages of all samples with the metrics command, eliminating any poor-quality samples and choosing a larger or smaller antitarget bin size if necessary. Build an updated pooled reference using batch or coverage and reference (see Copy number calling pipeline), coordinating your work in a Makefile, Rakefile, or similar build tool.
Based on the description above it seems that I should be able to inspect the statistical summary of all my normal samples and choose which ones to use to build the pooled reference.
I ran the "batch" command with just the normal samples as mentioned above and I get a targetcoverage.cnn and an antitargetcoverage.cnn file for each normal sample (I do not get a pooled reference file).
1) According to the documentation on using the "metrics" command there isn't an example that just uses the targetcoverage.cnn and antitargetcoverage.cnn files. How should I run the "metrics" command?
2) After I successfully run the analysis above, what should I be looking for in the output of the "metrics" command?
3) To build a pooled reference using the quality normal samples do I just use the "batch" command? Can I specify a different number of tumor and normal samples in the "batch" command?