I am attempting to generate a consensus sequence using the galaxy platform. I have been able to generate a pileup using Mpileup however I have been unable to generate a consensus sequence. I have tried using the instructions found in How to generate a consensus fasta sequence from SAM tools pileup? however Galaxy is not recognizing the results of the NGS: SAM Tools -> Pileup-to-Interval as a format that can be utilized for the final suggested step of Fetch Sequences -> Extract Genomic DNA. I have attempted to convert the data again to no avail. I'm at quite a loss at the moment. I would appreciate any insight or tips anyone could provide.
I think you are confused about the "extract genomic DNA" tool. You supply a list of intervals and this tool will fetch the reference sequence between these coordinates. For generating a consensus sequence you'll need to take a different approach - one that I'm not sure you'll find in Galaxy.