Question: Reference genome: no options available - use Custom reference genome
gravatar for a.donato
5 months ago by
a.donato0 wrote:


I am using galaxy and in particular a modified version of a workflow that I found on

Even if in the workflow I have everywhere indicated which one is the reference genome I wish to use, some steps such as the "Realigner target creator" on data coming from the step "Add or replace groups" give me a error because in the using reference genome section there are no options available and I don't know why that's happening and how to fix it.

Can anyone with more experience than me explain me how I should proceed?

Thank you.

Best regards. Alessandra

ADD COMMENTlink modified 5 months ago by Jennifer Hillman Jackson23k • written 5 months ago by a.donato0
gravatar for Jennifer Hillman Jackson
5 months ago by
United States
Jennifer Hillman Jackson23k wrote:


GATK tools are deprecated in Galaxy. Alternative tools for variant analysis are in our tutorials here:

If you do run into a tool that does not have your genome natively indexed on the server you are working on, a Custom reference genome can be used. This is how:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 5 months ago by Jennifer Hillman Jackson23k
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