CNVkit: not export cnr file

Question

[kkatoibaraki]

I try to detect tumor copy number variation using CNVkit installed via Bioconda ( https://bioconda.github.io/recipes/cnvkit/README.html ) under the description shown in URL ( https://cnvkit.readthedocs.io/en/stable/quickstart.html ). The command "cnvkit.py fix" does not produce sample.cnr file at all. I would like to know how to bulid sample.cnr file.

[kkatoibaraki]

The command "cnvkit.py fix" seemed to print lines of characters and numbers like sample.cnr data on the console.

[kkatoibaraki]

Thank you very much for your quick reply. I have designated the output directory and the output file using additional augment "-o", however, the output file did not appeared in the directory. I am looking forward to hearing from everyone. I appreciate your kindness in advance.

[GenoMax]

Use ADD REPLY/ADD COMMENT when responding to existing posts to keep threads logically organized.

[kkatoibaraki]

I am very sorry for misleading comments. I will try to do so next time.

Answer 1

[Kevin Blighe]

You need the -o option.

From the manual:

cnvkit.py fix Sample.targetcoverage.cnn Sample.antitargetcoverage.cnn my_reference.cnn -o Sample.cnr

Kevin

[kkatoibaraki]

Thank you very much for your kind comment. Now I am trying to analyze using hg19 as reference according to suggestions by developer.