It looks like you're new here. If you want to get involved, click one of these buttons!
A new tool has been released!
Check out the documentation at CGVarToVCF.
any example command?
If you follow the documentation link you'll find the necessary info to make a command.
Geraldine Van der Auwera, PhD
Hi. I couldn't run CGVarToVCF. when I give the options, -T CGVarToVCF, says can't find CGVarToVCF. Could you please give me an example to run CGVarToVCF. I need that tool badly. I have master file file,reference file and I want to convert it to VCF. Thanks in advance.
Actually this is part of our internal suite of tools; the document was made public by mistake. I'll see if it's possible to make the tool available to the public, but at the moment it's normal that you can't access it, sorry.
Update: there is no plan to make this tool public, largely because it is only a stopgap solution for the problem that CG's output format is badly designed and we cannot support it. We recommend that you contact Complete Genomics and request that they provide a better, preferably standardized output format like VCF.
Any chance you could reconsider releasing the tool? I'm in the same boat, as well - and as much as I'd like to request a better format, it doesn't really help my current situation.
We've discussed it and unfortunately we won't release it because we don't have the resources to test and maintain it. However, we do sympathize with your situation, and we are willing to give you the code so that you can add the functionality yourself to your local copy of the GATK. Please be aware however that we make no guarantees and you should only use it as a reference if you are willing to write code, not use it as a black box tool. If you are still interested despite all these caveats, let me know and I will send it to you.