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etal / cnvkit

Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
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cnvkit.py export #658

Closed lmanchon closed 2 years ago

lmanchon commented 3 years ago

-- Hi,

i have used export command as: cnvkit.py export bed ERR5873785.call.cns --show all -y -o ERR5873785.bed so i get this output: chr1 12098 125311770 ERR5873785 2 chr1 143125769 149887366 ERR5873785 3 chr1 149887521 152213599 ERR5873785 2 chr1 152213599 152353586 ERR5873785 4 chr1 152353586 248918365 ERR5873785 2 chr2 41567 86865444 ERR5873785 2 chr2 86866237 95882387 ERR5873785 3 chr2 95884158 106193584 ERR5873785 2

what the numbers in last column mean ? there are only positive numbers from 0 to n. How to assign duplication, deletion to these numbers ?

thank you --

tetedange13 commented 3 years ago

Hi @lmanchon,

I may be wrong, but CNVkit documentation mentions:

If the input .cns file contains a “cn” column with integer copy number values, as generated by the call command, export bed will use those values.

=> So as you are running cnvkit.py export bed on your ".call.cns", I guess this the copy number value attributed to each segment (derived from log_ratio) => Plus as you specified --show all, you are getting every segment, even ones with no CNV (CN=2)

Hope this helps. Felix.

lmanchon commented 3 years ago

so if I have CN <= 2 it's a deletion (loss) CN=2 --> no CNV and CN > 2 --> duplication (gain)

tetedange13 commented 3 years ago

Yes, if you are working on a diploid sample!