Does Galaxy have a tool that can filter a VCF file annotated with Ensembl VEP. If so could someone give an example of doing so.
Yes!
Start with bcftools split-vep plugin Extracts fields from structured annotations such as INFO/CSQ. See the examples that are on the tool form (scroll down into the Help section). The links out will have more. Any of those should work in Galaxy the same way.
After, (or you can query directly without the first step!), you can use VCFfilter filter VCF data in a variety of attributes to filter any VCF file. The queries can be custom. This tool also has examples on the tool form, and we have a tutorial example here:
- Hands-on: Calling variants in non-diploid systems / Calling variants in non-diploid systems / Variant Analysis (hands-on-filtering-vcf-data)
It seems the bcftools split-vep tool is only available at UseGalaxy.eu for now, so working there would be a good idea. I’ll make a ticket to have it installed at the other UseGalaxy servers.
Remember you are welcome to have an account at all of the public servers! And it is easy to move data between servers by URL if you want to access the slightly different resources at each.
Overall, I would suggest finding a protocol that does this so you can learn about which fields are usually queried to answer the kind of questions you have. The bcftools resources are probably where I would start, so that’s what I suggest now.
Please let us know if this helps! 
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@jennaj Thanks. That was very helpful. I successfully used the bcftools split-vep tool on my VCF so I shouldn’t have any issues doing the filtering now.
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Great! Glad you found it already!
I’ve also made the request to add that tool to the other servers.
I’m glad you asked! Sometimes a tool slips through the install. Finding those helps us to make the servers host a consistent tool kit (when possible!). 