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 ___________________________________________________________ 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: http://galaxyproject.org/search/mailinglists/