Hi, I'm trying to use cnvkit python package to calculate copy numbers for targeted amplicon sequenced data. I have cancer samples and normal samples and would like to do a paired reference, is this possible to do with cnvkit and how do I do it? In the documentation I only find examples for TAS without the usage of normal samples.
example: cnvkit.py reference *.targetcoverage.cnn --no-edge -o ref-tas.cnn
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written
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ingrid.schulman •
1 answer
Yes, the pipeline is nearly the same, but skipping the antitarget parts in coverage, fix, and reference.
With the batch command, use the option -m amplicon to run the whole workflow with reasonable defaults.
In the examples here, you can include a pool of normal samples with the -n flag, as in the standard pipeline.
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