Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
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.

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.


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