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Question: GATK in galaxy
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gravatar for jeevanbio7
22 months ago by
jeevanbio7 • 0
jeevanbio7 • 0 wrote:

whenever i try to run GATK in galaxy Im getting this following error "Sequences are not currently available for the specified build." in the BAM input file..how to execute GATK in galaxy please help ASAP
galaxy gatk • 804 views
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modified 22 months ago by Jennifer Hillman Jackson ♦ 25k • written 22 months ago by jeevanbio7 • 0
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gravatar for Jennifer Hillman Jackson
22 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

If working at http://usegalaxy.org, the GATK tools have been deprecated. This means that no additional genomes will be indexed for the tool and other errors might occur. The tools are left on the server as a convenience.

If working at another site, then the genome assigned to your data can be used a Custom reference genome that is set up as a Custom Build (assuming the site supports Custom genomes/builds). Or, the genome could be added as a native index for the tool using a Data Manager (sourced from the Tool Shed like other tools - a better choice if this is your own Galaxy, you are admin, and will be doing multiple analysis runs using the same genome).

Help: https://wiki.galaxyproject.org/Support#Custom_reference_genome

Thanks, Jen, Galaxy team
ADD COMMENT • link written 22 months ago by Jennifer Hillman Jackson ♦ 25k
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