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Question: Galaxy workflow RealignerTargetCreator reference genome not available
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gravatar for jannetta.steyn
2.8 years ago by
jannetta.steyn • 10
jannetta.steyn • 10 wrote:

I am (still) trying to implement the GATK best practises pipeline using Galaxy workflows. I managed to align using bwa and then I managed to run Picard MarkDuplicates. Now I want to run RealignerTargetCreator. This leads to three questions:

  1. Why is NGS GATK Tools marked as beta?
  2. Why is NGS GATK Tools shown as deprecated?
  3. When I select RealignerTargetCreator in the NGS GATK Tools section I get no reference genome in the drop down box. Why not?

Any help will be appreciated.

Kind Regards

Jannetta

 
galaxy • 649 views
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modified 2.8 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.8 years ago by jannetta.steyn • 10
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gravatar for Jennifer Hillman Jackson
2.8 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The best current versions of GATK tools are available in the Tool Shed for use in a local or cloud Galaxy.

https://wiki.galaxyproject.org/BigPicture/Choices

http://usegalaxy.org/toolshed

The version at http://usegalaxy.org is v1.4 and is no longer supported. If you still wish to use it, there could be problems in certain cases that will not be fixed because of the other updated versions (errors should not be submitted as bug reports). The natively indexed reference genome is from 1000 Genomes, which is database assignment hg_g1k_v37. The option to use a Custom reference genome/build is the alternative for other genomes. Using a large genome such as hg19 is known to exceed memory resources at the public server and is not recommended.

Thanks, Jen, Galaxy team
ADD COMMENT • link written 2.8 years ago by Jennifer Hillman Jackson ♦ 25k
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