Hi Jen,

Thanks a lot for spending time again on my issue !
I think I will go for command-line solution !


Le 03/12/2013 00:43, Jennifer Jackson a écrit :
> 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

Fabrice Besnard
Institute of Biology of the Ecole Normale Supérieure (IBENS)
46 rue d'Ulm, 75230 Paris cedex 05, France
8th floor. Office: Room 802. Lab: Room 817.
mail: fbesn...@biologie.ens.fr
Tel: +33-1-44-32-39-31
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