I have just get my CNV files by CNVkit. I am wondering if the column "log2" in the output of CNVkit (after call) is the same as "Seg_mean". If not, how can I get the "Seg_mean" with "log2"? Please, give me some advice,thanks!
Please read: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002202 and add more relevant details to your question. What have you tried? Have you read the CNVkit paper?
Here are two lines of what I get.
chromosome start end log2 probes
chr1 826717 2410579 -0.00659771 487
chr1 2410780 2787772 -0.372291 70
Yes, I have read the CNVkit paper,here is the link: https://cnvkit.readthedocs.io/en/stable/pipeline.html#call
I get an answer like this :Segment_Mean is the arithmetic mean of those probes' log2 copy ratio values.
But I am still confused how can I get "Segment_Mean"? I need it as an input to ABSOLUTE.
And I have got CNV file by Varscan too ,but the "Segment_mean" is quite too large.
I've moved this to a comment - please do not add an answer unless you're answering the top-level question. Plus, edit your question and add this information in there. Please read posts under /t/how-to for more information.