Question: CNVkit output problem: Is "log2" the same as "Seg_mean"? OR how can I get "Seg_mean" with "log2"?
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gravatar for 948077241
7 weeks ago by
9480772410
9480772410 wrote:

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!

cnv cnvkit seg_mean • 123 views
ADD COMMENTlink modified 7 weeks ago • written 7 weeks ago by 9480772410

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?

ADD REPLYlink written 7 weeks ago by RamRS20k

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.

ADD REPLYlink modified 7 weeks ago • written 7 weeks ago by 9480772410

And I have got CNV file by Varscan too ,but the "Segment_mean" is quite too large.

ADD REPLYlink written 7 weeks ago by 9480772410

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.

ADD REPLYlink modified 7 weeks ago • written 7 weeks ago by RamRS20k
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