How to use GATK Unified Genotyper with "A list of genomic intervals over which to operate" option
Hi, I would like to run "Unified Genotyper" on a region of a BAM file, I see the advance option "A list of genomic intervals over which to operate" exist and seems to be what I need. The problem is I only get a drop-down menu with the single option "Selection is optional", which I don't understand. Thanks, Carlos
Hello Carlos, This tool is still under development on the test Galaxy instance and not all features/functions are complete. This is one of them and there are a few others like it. Please be aware that there could potentially be other as yet uncovered issues with the tool. Just wanted to send a reminder. This is true for all tools on the Test server, even those that are published onto main could possibly be undergoing changes on test. Hopefully this helps to explain what is going on. If you do notice anything else that you think is wrong with the tool or its output (should you continue to test-drive it), we would be glad to have your feedback/comments. Take care, Jen Galaxy team On 9/12/11 2:13 PM, Carlos Borroto wrote:
Hi,
I would like to run "Unified Genotyper" on a region of a BAM file, I see the advance option "A list of genomic intervals over which to operate" exist and seems to be what I need. The problem is I only get a drop-down menu with the single option "Selection is optional", which I don't understand.
Thanks, Carlos ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
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participants (2)
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Carlos Borroto
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Jennifer Jackson