If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Automate Oncotator using command line access ?
Respected Sir / Ma'am,
Our team is working on NGS, we are using oncotator frequently. Thank you for great tool.
I am working on automating our NGS process, hence I nedd to submit job using command line and hence download result as well.
Is there any script or command which can automate submiting job to online server and get result as well ?
CRAVAT provide web services (http://www.cravat.us/help.jsp?chapter=report_help&article=top). We have write curl script to submit job online and to download result.zip. I was able to do that.
So is this type of automation available for Oncotator ?
Waiting for positive reply.