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etal / cnvkit

Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
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Can't convert to gistic marker due to input validation #776

Closed FriederikeHanssen closed 11 months ago

FriederikeHanssen commented 1 year ago

Hi,

thank you for providing cnvkit and also funcitons to make the ouput compatible for gistic. It is really great to have that.

I ran the seg command just fine according to the docs, however I am not able to run the markers file generation:

cnvkit.py export gistic ../cnr/*.cnr -o samples.gistic.m

leads to error:

usage: cnvkit.py export [-h] {bed,seg,vcf,theta,nexus-basic,nexus-ogt,cdt,jtv} ...
cnvkit.py export: error: argument {bed,seg,vcf,theta,nexus-basic,nexus-ogt,cdt,jtv}: invalid choice: 'gistic' (choose from 'bed', 'seg', 'vcf', 'theta', 'nexus-basic', 'nexus-ogt', 'cdt', 'jtv')

looks like the validation in the beginning failed. Or I am using the command wrong.

I am using cnvkit version 0.9.9.

Thank you for any hints on how to get it to run :)

tetedange13 commented 1 year ago

Hi @FriederikeHanssen ,

This issue is know and were fixed, but after release of CNVkit v0.9.9 => Until next release, you will have to use most updated CNVkit code from master branch (cloning repository or dowloading ZIP code)

Hope this helps ! Have a nice day, Felix.

FriederikeHanssen commented 1 year ago

Thanks for getting back to me so quickly! Alright, I will check the master branch and otherwise wait for a new release :)

FriederikeHanssen commented 1 year ago

Is the release with the fixed already planned? Just asking because for the analysis a tagged release would be preferable :)

FriederikeHanssen commented 11 months ago

was added to 0.9.10 release so closing it.