Can we use the SAM tools pileup tool in Galaxy to get an accurate count of the coverage across the genome? I ask because I have  run the pileup tool in Galaxy with bam files generated from tophat  and  noticed that the coverage reported in the pileup data was consistently lower then what I see in IGV. For example, I look at chr_1, coordinate 3515 and I see 10 reads mapped to that coordinate. I look in the pileup and it reads 1x coverage.    I have not applied any filter to the pileup because all I want is a readout of the coverage at each NT including the number of variants that occur. My settings were do not print mapping quality, print all lines, cap mapping quality to- 0, call consensus according to MAQ model- NO. Any suggestions?  Is there a tool in Galaxy other than  pileup that can do this?

Thanks, 

Patrick