Hi Fabrice,

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-galaxy-callable-base-and-depth-of-coverage-after-bqsr

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:
Hi all,

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,

Fabrice


--
Jennifer Hillman-Jackson
http://galaxyproject.org

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