Need help with selecting reference genome in Galaxy installed locally

[manojmw]

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.

[jennaj]

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.

Galaxy Training: Variant Analysis

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

@manojmw

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.

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:

Indexing reference genomes with Data Managers: Resources, tutorials, troubleshooting

Hi, The mm10 reference genome/build is sourced from UCSC. You’ll need to index the genome on your server with Data Manager tools. Install the genome with Data Managers (sourced from the ToolShed, all are in a separate category there). Install DMs like any other tool using the Admin functions. You’ll need these DMs at a minimum. Execute them in this order first: Fasta fetcher – has an option to pick UCSC as the data source. SAM indexer Picard indexer 2bit (twoBit) indexer Then get the DMs…

Alternative to DM tools for inbuilt reference sequence

What are your goal(s)? Install reference genomes into your own Galaxy server? Learn the source of a particular reference genome available at a public server? Exact sequence data from a reference genome (based on coordinates) that is already indexed on a server you are working on or some custom reference genome fasta you have in your history? Other? Running Data Managers to install genomes is an administrative function, and these can be run with web-based tools or line-command. You would need…

Thanks!

[manojmw]

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

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