Need help with selecting reference genome in Galaxy installed locally

Hello everyone,

I am trying to annotate a VCF file containing the sample data to predict the genes with polymorphic sites. I am using ANNOVAR tool. But, no options are available for me under Gene/Annotation/Databases in order to annotate.

I am running galaxy locally and for most of the tools, there is no option available to select reference. I am finding it really difficult to proceed with my work.

ANNOVAR tool

46: VCFfilter: on data 45
Gene Annotations
Select/Unselect all
No options available

Annotation Regions
Select/Unselect all
No options available

Annotation Databases
Select/Unselect all
No options available

Could someone please help me out?

Thank you.

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Hello @manojmw

The human hg19 is the only genome build with reference annotation available with Annovar. The input VCF dataset must be based on the hg19 build and have that database assigned.

Alternatives are covered in these GTN tutorials.

You can also review the tools under the VCF/BCF and Variant Calling tool groups at usegalaxy.org for more options.

When working at your own Galaxy, genomes and indexes need to be installed. Use Data Manager tools. I added some tags to your post that point to prior Q&A concerning the use of DM. Note that not all tools have a Data Manager, and Annovar is a tool that does not have one.

Start here:

Thanks!

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Thank you very much @jennaj for such a quick response.

I will look into the solution provided by you and let you know :slight_smile:

1 Like