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.
dbSNP_RS seems to not be annotated with Oncotator 1.9.3
Oncotator 1.9 seems to not be annotating dbSNP annotations (dbSNP_RS), leaving all elements blank in this column. Other annotations are correctly annotated.
My command line is oncotator -v --db-dir /Database/oncotator_v1_ds_April052016/ test.mutect.txt test.snv.maf hg19