Description
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 :)