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,