CNVkit reference.cnn .cnr .cns log ratio

Question

[nina.naitatmane]

hello, I'm trying to use cnvkit on ion torrent ngs data to detect CNVs. i'm not biologist at all, I have vague knowledge about CNVs, that's why i'm looking for someone who can help me to understand what is the reference.cnn file? and what are file extension .cns and .cnr? inorder in interpret them. any other information or link is welcome (french or english). Thank you .

Answer 1

[Eric T.]

Here's the documentation for CNVkit's formats: http://cnvkit.readthedocs.io/en/stable/fileformats.html#target-and-antitarget-bin-level-coverages-cnn

In a nutshell, these are just tabular formats with column headers that can be easily loaded in R or Python (pandas).

• reference.cnn is the copy number control used for normalization of test samples.
• .cnr means normalized copy ratios. These are processed test samples, already normalized to the reference.
• .cns means copy number segments. These are the result of segmenting .cnr files, essentially where bins with similar estimated copy number are joined together.