I know I already replied to your other post about this tool and the status/reasons why it is not wrapped in Galaxy right now, but I was going to suggest that you ask on the GATK forum for help about using the "CallableLoci" tool on the command-line since you asked again. Then I checked for prior Q/A and I saw that you were a step ahead and already found advice on 11/8: http://gatkforums.broadinstitute.org/discussion/3448/unified-genotyper-with-...
This really is the best advice, including the coverage part of the question there. As long as you are an acedemic/non-profit user, there should be no licensing issues using the tool directly.
I didn't see anything posted at seqanswers, and that can often be another source of information, but I would have to agree with Geraldine that going command-line with the "CallableLoci" tool is probably your best option since this is the exact data that you want, and I am not aware of any web-based implementations.
But, this is still open for others to comment on! The web is a big place & all input is welcome.
Good luck with your project!
Jen Galaxy team
On 11/25/13 8:59 AM, Fabrice Besnard wrote:
Would someone know how to get the information on which areas of the genome are considered callable after a call with Unified genotyper from GATK (as a .bed or pileup file)?
Thanks for your help/advice,