Question: Sam Tools Pileup
0
Patrick Kenneth Gonzales • 20 wrote:
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?
Thanks,
Patrick