I changed the workflow to use my own uploaded reference file, not the built-in index, but judging from the nomenclature I suspect I may have to process (index?) the reference file first into a format usable by the pileup generation tool. However I do not see how I can do that.
Galaxy should do this automatically. At least it did it for me yesterday (admittedly using SOLiD data instead of Illumina. I still recommend manually running each step instead of relying on a workflow. -- Rick Westerman westerman@purdue.edu Bioinformatics specialist at the Genomics Facility. Phone: (765) 494-0505 FAX: (765) 496-7255 Department of Horticulture and Landscape Architecture 625 Agriculture Mall Drive West Lafayette, IN 47907-2010 Physically located in room S049, WSLR building