Question about run cnvkit on DNAnexus

Question

[qyang]

I met a problem. I want to run the app CNVKit on DNAnexus in CLI. The command I want to execute is from the manual of CNVKit, which is cnvkit.py call Sample.cns -y -o Sample.call.cns

The name of cnvkit.py on DNAnexus is cnvkit_batch

So I tried: dx run cnvkit_batch call COt1049.cns -y -o COt1049.call.cns

But it does not work.

I have checked the help page for cnvkit_batch, it does not tell me how to specify the command "call".

Answer 1

[Eric T.]

The public app on DNAnexus just runs the standard pipeline, equivalent to CNVkit's batch command. The app doesn't provide a way to run sub-commands like call.

However, the only step of the pipeline that is particularly resource-intensive is the coverage command, which is the first step in batch. Once you have the .cnn files from the cnvkit_batch app (and ideally .cnr and .cns, to save yourself some typing), you can easily run the rest on a laptop, even for WGS data. Try installing the cnvkit package with conda/Anaconda, or use the Docker image if you prefer. Either installation approach will give you access to the call command and the rest of CNVkit's functionality.