Question: Realigner Target Creator (GATK) with a custom or native local genome
gravatar for Joan Gibert
10 months ago by
Joan Gibert20
Joan Gibert20 wrote:


I cannot introduce any local reference genome in the Realigner Target Creator. Is this because is beta?

Thanks! Joan

snp genome gatk custom freebayes • 404 views
ADD COMMENTlink modified 10 months ago by Jennifer Hillman Jackson25k • written 10 months ago by Joan Gibert20
gravatar for Jennifer Hillman Jackson
10 months ago by
United States
Jennifer Hillman Jackson25k wrote:


Please be aware that the GATK tools wrapped for Galaxy, all versions, whether from the Tool Shed or still hosted on a public server, are considered deprecated and are no longer supported. This means that any might not install correctly or fail for odd reasons. The GATK Data Managers intended to install built-in indexes on a local Galaxy are known to not function correctly.

The Galaxy variant analysis tutorials cover alternative tools/workflows:

That said, some GATK tools may still function. To use a custom genome, set the first option on the tool form Choose the source for the reference list as History. All datasets with the fasta datatype assigned will then show up in the Using reference file option select list.

How to make sure a custom genome is formatted correctly:

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 10 months ago • written 10 months ago by Jennifer Hillman Jackson25k
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