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TurakhiaLab / rivet

SARS-CoV-2 Recombination Viewer and Tracker
https://rivet.ucsd.edu/
MIT License
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Updating README for vcf generation? And general question. #2

Closed charlesfoster closed 1 year ago

charlesfoster commented 1 year ago

Hi,

The README says: "Please see the following workflow to create a VCF for uploading to RIVET locally." This link is currently dead. Are there some instructions prepared to describe how to create the VCF file locally? From reading run_ripples_filtration.sh, I believe that least the first command may be matUtils extract -i $mat -s filtering/data/allRelevantNodeNames.txt -v filtering/data/allRelevantNodes.vcf -T 10. Is this correct? And is it possible to run the frontend without running the rivet pipeline using the results from ripples, or is that not recommended?

Finally, are there any plans to enable running rivet entirely locally without using Google Cloud?

Thanks, Charles

mrkylesmith commented 1 year ago

Hi Charles,

Thanks for the issue! You are correct, matUtils extract is the command to use and I have updated the link to create a VCF so please see that page for specific details on generating a VCF that can be uploaded to the RIVET frontend locally.

Yes it is possible to run the RIVET frontend locally (with reduced functionality compared to https://rivet.ucsd.edu/) with results from ripples ( we recommend using ripples-fast), although you will need to rearrange the columns of the recombinants.tsv output file from ripples. The RIVET frontend requires an input tab-delimited results file (-r) with the first 3 columns being the recombinant node id \t donor node id \t acceptor node id. Please see this section of the readme: Viewing your own recombinants with RIVET on a local HTTP server

For more information on the quality control and filtration pipeline that is part of the RIVET backend, please see our About page and also Pandemic-scale phylogenomics reveals the SARS-CoV-2 recombination landscape, which provides more details.

And yes, we do plan to support this, the ability to do this should be available to users by next week (along with a few other new features), stay tuned!

Best, Kyle

charlesfoster commented 1 year ago

Thanks for the info. I'll stay tuned!