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 for generate pileup 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?

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