Hi Fabrice,

This tool is not implemented in Galaxy as it was released after the current GATK (beta) tool group was created.

There is some development on the last GATK-lite pipeline, but as you know this does not include the latest version of all tools. The public Main Galaxy server (usegalaxy.org) only contains tools that are licensed for general use, no restrictions.

One option is to use the tool command-line, then upload the results into Galaxy for use with our other tools to compliment/incorporate it into your larger analysis. There is much help offered on the GATK forum, and this is just one tool. So, even if you are experienced with bioinformatics on the command-line, this might be possible. You seem to be very knowledgeable about these tools and how they function! My guess is that you'll be able to pick this up!

Sorry that we could not help more directly right now. But please follow this Trello ticket to watch upcoming GATK tool wrapper development by the Galaxy team. If this specific tool does turn out to be added in the lite implementation, this is a great way to know when to look for it: https://trello.com/c/IPkT2spd

Best!

Jen
Galaxy team

On 11/20/13 2:25 AM, Fabrice Besnard wrote:
Hi all,

First of all, thank you again for all your efforts to develop a project
like Galaxy, that makes leading-edge bioinformatic tools available for
non-bioinformaticians and wet-lab biologists like me !

I am using GATK Unified Geneotyper through the Galaxy main server to
analyze variations from whole-genome re-sequencing data.
I have read in the GATK documentation that there is a tool called
"CallableLoci", that gives a .bed file of the genome indicating
specifically which base where callable or not by Unified Genotyper (UG),
using different criteria such as read depth, base quality, mapping quality.
The log & metrics files generated by UG in Galaxy give the general
statistics of callable loci, but there is no such a file giving a
detailed information of the eligibility of each base.

Right now I am using the tool "depth of coverage on BAM file" to get an
idea of this information, but it's only partial since it doesn't take
into account all the parameters used by UG to consider a locus callable
(notably base quality and mapping quality).

Do you think it would be possible to implement the "CallableLoci" tool
in Galaxy?
Would someone propose me an alternative to get this precious information
on which areas of the genome are considered callable ?

Thanks for your help/advice,

Fabrice

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Jennifer Hillman-Jackson
http://galaxyproject.org

___________________________________________________________
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:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

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