Question: What to write in "Using reference genome" and "Annotation Regions"sections ?
gravatar for Amir.saeidian
3 months ago by
Amir.saeidian0 wrote:

Hey, I am trying to use GATK through Galaxy and trying to call variants from my vcf file. "Select Variants from VCF files (Galaxy Version 0.0.3)". What to write in "Using reference genome"? I have another issue while using ANNOVAR for annotation. What to write in "Annotation Regions" and "Annotation Databases"? Thanks

ADD COMMENTlink modified 3 months ago by Jennifer Hillman Jackson25k • written 3 months ago by Amir.saeidian0
gravatar for Jennifer Hillman Jackson
3 months ago by
United States
Jennifer Hillman Jackson25k wrote:



  • All of Galaxy's currently wrapped GATK tools are considered deprecated, are based on older GATK releases, and may fail for a variety of reasons. For now, skip using GATK in Galaxy, whether at a public server or your own local Galaxy with the tools loaded from the ToolShed.
  • It is better to use the latest Variant Analysis protocols. Please see the Galaxy Tutorials here:
  • There are development plans to wrap the newer GATK release's tools, but that is still a work in progress.


  • Only a limited number of genomes are supported by the tool as available at most public Galaxy servers.
  • At, hg19 is supported. Given a VCF input both based the hg19 genome/build and assigned that database, a listing of available selections will show up for those tool settings.
  • FAQ explaining how to assign metadata, including "database": >> How do I find, adjust, and/or correct metadata?
  • Important: The data content (not just the database assignment) must actually be based on the hg19 genome/build/version, otherwise, the tool will end with an error due to a genome mismatch. In other words, avoid assigning that database in hopes that it will retrieve annotation for VCF content based on a different genome/build/version.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 3 months ago by Jennifer Hillman Jackson25k
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