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etal / cnvkit

Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
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Make clear in the documentation that the batch command is also running "call" #736

Open LukaP-BB opened 2 years ago

LukaP-BB commented 2 years ago

In https://cnvkit.readthedocs.io/en/stable/pipeline.html#batch, a code example summarize the steps that the batch command runs, but forgets at least about the "call" aspect. This is a bit confusing when a file .call.cns appears in the outputs. Since we don't have control over the call options through the batch command, I wonder how relevant it is to have this function running in the pipeline ?

haydenshinn commented 1 year ago

I also ran into this issue and was extremely confused until I had to look through batch.py and saw that it ran "call" like you mentioned. They definitely need to update the batch examples/documentation and explain that.

WandaC-S commented 1 year ago

I am also confused. With batch.py, I get .call.cns and .cns, but the log2 value is different in the two files. Then I use "call" with default parameter, I got different cn number.

tetedange13 commented 1 year ago

Hi all,
CNVkit documentation were updated a few months ago and these information were added : => However the link present in CNVkit main repo page (= http://cnvkit.readthedocs.org/) automatically send towards stable version of the documentation (which dates of v0.9.8)

To get most updated version on Read The Docs, you have to go to the bottom left of the page and select master instead (direct link : https://cnvkit.readthedocs.io/en/master/) => You should see more detailed information about batch subcommand inside Copy number calling pipeline section

@etal, maybe there is something that you can change here ? Edit this link towards documentation to start ? => Also I do not see any available documentation for latest release v0.9.10 (and shown latest is not actually up-to-date)
Kind regards, Felix.

WandaC-S commented 1 year ago

@tetedange13 I am a beginner of CNV analysis. Thanks very much for your reply, now I can see the latest document in master page. I run pipelines for WES data, use the --method option with value amplicon.
Could you please explain why you add "# Post-processing for each tumor sample..." which process likely two-run segmetrics/call/bintest ? What is the difference between call.cns got with batch.py and default call like "cnvkit.py call mytumor.cns -y -m threshold -t=-1.1,-0.4,0.3,0.7 -o mytumor.call.cns"? Or should I just use the call.cns got with batch.py?