Using cnvkit for targeted amplicon sequencing

Question

[ingrid.schulman]

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

Answer 1

[Eric T.]

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.