What free Galaxy instance has a working SNPEff and other annotation and VCF processing tools to process a human genome data? Need to do annotation of a a thyroid cancer patient. Tried using VEP and wAnnovar, looking for more software. Thx.
Please see the Galaxy tutorials here: https://galaxyproject.org/learn/
Those at the top can be run at Galaxy Main https://usegalaxy.org.
Tutorials from the Galaxy Training Network (GTN) can be run entirely in the provided docker image (when available), your own local/cloud/docker Galaxy, and sometimes (or mostly) at Galaxy Main and/or Galaxy Europe https://usegalaxy.eu. Options: https://galaxyproject.github.io/ Choices: https://galaxyproject.org/choices/
Other public servers can also be reviewed, several are domain specific: https://galaxyproject.org/public-galaxy-servers/
Related question: https://biostar.usegalaxy.org/p/27172/
SnpEff is problematic for some use cases and the tool authors are still working on the correction. However, Human (hg19, hg39) works fine with SnpEff.
Details: The problem with SnpEff is specifically related to nested genomes in the SnpEff data source, and these are generally smaller non-mammalian genomes. The index retrieval tool will not work publically anywhere that I know of. You would need to install the older version of the tool and the related indexes in your own Galaxy (not through the SnpEff index retrieval tool) and then test it. The older version has been reported to work correctly, but that has not been confirmed. Ticket: https://github.com/galaxyproject/tools-iuc/issues/1354
Thanks! Jen, Galaxy team