3.5 years ago by
When using the public Main Galaxy instance at http://usegalaxy.org, this tool is natively indexed for the reference genome "hg_g1k_b37" when using the option "Choose the source for the reference list: Locally cashed". This is the 1000 genomes version of the GrCH37 Human build, sorted in a "GATK" specific manor.
If not using this specific build or if there is a mismatch, the problem you describe will result with this tool. Specifically, when using "Choose the source for the reference list:" as "locally cashed" with nothing selected for ""Using reference file" or if hg_g1k_b37 is a mismatch for the input. Or when using "Choose the source for the reference list:" as "history" without specifying a Custom reference genome (option "Using reference file: <fasta dataset in your history>").
More about Custom reference genomes:
Perhaps one of these is the issue? Please examine the form parameters you used (click on the "re-run" icon, the blue double arrow in the dataset box) to check, and adjust as needed.
These tools (all of GATK Beta - v1.4, or you can try GATK2), can be used on a cloud or production local Galaxy, where additional local reference genomes can be added (necessary for larger genomes - smaller Custom reference genomes tend to work best with this tool due to the resources it requires). Should you decide to go this route, here are some links to get started:
http://usegalaxy.org/cloud or http://getgalaxy.org (Galaxy)
http:///usegalaxy.org/cloud (Tools, these and many others)
Please let us know if you need more assistance, Jen, Galaxy team