Question: Sam Tools Pileup
gravatar for Patrick Kenneth Gonzales
6.9 years ago by
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
galaxy • 1.1k views
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