Dear all,
I have run cnvkit using WGS data, and gene regions were provided as targets. And I get output.cnr like this:
chr start end gene log2 cn depth weight
1 44288 46137 gene027230 -0.126498 2 11.2612 0.805428
1 46137 47987 gene027230 -0.00296269 2 12.9805 0.822361
1 47987 49837 gene027230 -0.0577102 2 12.9541 0.831048
1 50876 52489 gene027231 -0.0192799 2 13.509 0.787347
1 52489 54102 gene027231 0.0389804 2 13.9628 0.788384
1 54102 55716 gene027231 -0.0985898 2 11.0235 0.722622
1 92298 93716 gene027232 -0.365783 1 11.0071 0.739006
1 93716 95134 gene027232 -0.037821 2 13.2454 0.754825
And I would like to know which gene is duplicated/deleted. How could I merge log2-values of bins that belong to the same gene? And is it reasonable that genes with log2-value > 1.0 were considered as duplications, and those with log2-value < −1.0 constituted deletions.
Thank you for your help
Songtao Gui
•
written
by
guisongtao0104 •
1 answer
To merge bins you need to run cnvkit.py segment to create .cns files.
Assuming a diploid genome:
- Log2(CR) = -1 → CR = 0.5 → 1 copy (of a segment/gene).
- Log2(CR) = 0 → CR = 1 → copies
- Log2(CR) = +1 → = 2 → 4 copies
- Log2(CR) = 0.58 → = 1.5 → copies
Of course you have to consider a bit of margin around those values to call deletions or amplifications: for example, you can assume that with Log2(CR) = -1.1 your organism still have you gene copy and with Log2(CR) = 0.4 you can be confident that it has 3 gene copies.
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