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TrinityCTAT / ctat-mutations

Mutation detection using GATK4 best practices and latest RNA editing filters resources. Works with both Hg38 and Hg19
https://github.com/TrinityCTAT/ctat-mutations
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Mutations in DEMO data not found #81

Open neoscreen opened 3 years ago

neoscreen commented 3 years ago

Hi Following the procedure of CTAT MUTATION in DOCKER, with the DEMO data from BroadInstitute, the cancer.tab file had only 4 mutations instead of the big list of mutations mentioned in the Table, at the end of this page https://github.com/NCIP/ctat-mutations/wiki/Walk-through-tutorial

brianjohnhaas commented 3 years ago

Thanks for reporting this. We changed much of the pipeline since the demo data was originally made available. I'll update the demo data shortly so that it's more relevant to cancer biology based on our latest annotation framework. (many of the earlier reported variants turned out to not be as cancer relevant as initially thought, even if they turned up in certain oncogenes). More soon.

neoscreen commented 3 years ago

dear @brianjohnhaas thank you for your reply. please email me about the new mutation list in order to check my installation and pipeline. Best regards,

brianjohnhaas commented 3 years ago

Sure thing. Here's the updated documentation and pointer to the sample data to use.

https://github.com/NCIP/ctat-mutations/wiki/Walk-through-tutorial

neoscreen commented 3 years ago

dear @brianjohnhaas it works like a charm ;). Thank you .. Yannis

brianjohnhaas commented 3 years ago

fantastic! That's what I love to hear. :-)

On Thu, Mar 4, 2021 at 5:48 PM neoscreen notifications@github.com wrote:

dear @brianjohnhaas https://github.com/brianjohnhaas it works like a charm ;). Thank you .. Yannis

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/NCIP/ctat-mutations/issues/81#issuecomment-791001829, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKX5A4TKVUYOKVHJ365DTCAE2HANCNFSM4YKKHBTA .

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