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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