Gviz Coverage Plot of bam file does not match Rsamtools pileup function

Question

[averysfeit]

Hello! I'm trying to figure out how gviz produces the coverage plot for AlignmentTracks. I am finding a mismatch between the gviz coverage plot and one produced using the Rsamtools pileup function. When plotted (using the plottracks function for the AlignmentTrack and a simple scatter plot for Rsamtools pileup), the coverage looks the same, but the numerical values are different.

Thank you!

Code for Rsamtools:

which <- GRanges(chr,IRanges(z_start,end + zoom_f))
what <- c("rname","qname", "pos","qwidth")

scanparam <- ScanBamParam(which=which, what=what)

pileupparam <- PileupParam(max_depth=250, min_base_quality=13, min_mapq=0, min_nucleotide_depth=1, min_minor_allele_depth=0, distinguish_strands=FALSE, distinguish_nucleotides=FALSE, ignore_query_Ns=FALSE, include_deletions=TRUE, include_insertions=FALSE)

bamfile <- BamFile(x.bam)
pileup <- pileup(bamfile, scanBamParam = scanparam, PileupParam=pileupparam )
scatter.smooth(pileup$count)

Code for gviz:

gtrack <- GenomeAxisTrack()
alTracks <- AlignmentsTrack(x.bam, name = 'x' , isPaired = paired, col = "#808080")
plotTracks(c(list(gtrack,unlist(alTracks)), 
               from = 38053189, to = 38069893 ,chromosome = 'chr14', main = 'ESR1', cex.main = 4, transcriptAnnotation = "symbol", 
               type= "coverage", fill.coverage = "dodgerblue", cex = 1, sizes = c(1,1,1,rep(3,length(alTracks)))
    )

[Friederike]

It'd probably be helpful to see the two outputs in question including the commands you've used for both samtools and Gviz

If you'd like to add the resulting plot, you can find instructions on how to include images here.