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.
How to restrict Oncotator annotations?
I am using Oncotator to add annotations to my germline VCF file and I'm unable to turn-off some tumor specific annotations. I have been looking for answers on GATK forums, but I couldn't locate the documentation that explains all the input flags. I did find this basic input article, but it's not a lot informative for my specific interest,
My current Oncotator command reads like this,
oncotator -v --input_format=VCF --output_format=TCGAMAF --db-dir $oncotator $workDir/$sample.variants.annotated.vcf $workDir/$sample.variants.annotated.onco.mafplus hg19
I would like to,
1. Turn off all the "UNKNOWN" columns
2. Turn off dbNSFP and ESP columns