Question: What free Galaxy instance has a working SNPEff and other annotation and VCF processing tools to process a human genome data?
0
gravatar for msprindzhuk
8 months ago by
msprindzhuk50
msprindzhuk50 wrote:

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.

ADD COMMENTlink modified 7 months ago by Jennifer Hillman Jackson25k • written 8 months ago by msprindzhuk50
0
gravatar for Jennifer Hillman Jackson
7 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

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

ADD COMMENTlink modified 7 months ago • written 7 months ago by Jennifer Hillman Jackson25k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 120 users visited in the last hour