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.
Refseq annotation for Oncotator
Oncotator uses GENCODE/ENSEMBL transcripts and annotations for hg19. Is there a way I could use RefSeq Transcript annotations instead. I am talking about 'cChange' and 'pChange' annotations. I do see RefSeq Transcripts annotated in a separate column in my current output file, but it seems 'cChange' and 'pChange' come from Ensemble Transcripts. Is oncotator flexible enough to shift to RefSeq Transcripts? The ideal solution would be to update oncotator's backend database to RefSeq. I couldn't find any auxillary tools in the oncotator directory that would allow me to update the backend. Please advice.