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:
- Why is NGS GATK Tools marked as beta?
- Why is NGS GATK Tools shown as deprecated?
- 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.