Having a few teething problems on my first use of Galaxy (surprise!)
Workflow as follows;
Upload fastq files (forward and reverse)
SAM to BAM
ANNOVAR gives an empty vcf file and on closer inspection, MPileup gives 55,000,000 lines form 3,600,000 in the sam.
MPileup appears to have called every base, each line looking like this;
The alt base is <X> for every base. I assumed it was a reference genome mismatch but I have done my best to use several reference genomes and I get the same (or similar) problem.