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Documentation for Oncotator running in Firecloud

dannykwellsdannykwells San FranciscoMember ✭✭

The output from the Firecloud oncotator does not match the output that is documented here:


Could you please direct me to where the documentation for the Oncotator version in Firecloud resides?

Best Answer


  • KateNKateN Cambridge, MAMember, Broadie, Moderator admin

    Hi @dannykwells,

    As we haven't heard back from you, I will be closing this ticket. Beri linked a few additional resources that may help, so if those don't fully answer your question, please reply back here with answers to Beri's questions above and we can take another look.

  • dannykwellsdannykwells San FranciscoMember ✭✭

    Hi @KateN - I'm a little confused, the response to my comment is gone from @bshifaw , as is my most recent question. Was something wrong in my previous post? Let me know if I can do anything. We are eager to figure this out.

  • KateNKateN Cambridge, MAMember, Broadie, Moderator admin


    I remember Beri's and your responses were here... I didn't delete them, so I'm thinking something went wrong somewhere. I'll look into that, and I apologize for the confusion.

  • KateNKateN Cambridge, MAMember, Broadie, Moderator admin

    @dannykwells As it turns out, Beri moved your thread to our GATK forum here, as the question was more about our tool documentation. Unfortunately, he misclicked and didn't move the entire thread, just select comments. You can follow up there for more information!

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