Pileup from Rsamtool missing snps in bam files

Question

[MAPK]

Hi Guys,

I am using pileup with the parameters as shown below. I am trying to get all the snps in bam file and the depth for those regions, but it does not give me all the snps. What am I missing here?

params <- ScanBamParam(
  which=which,
  flag=scanBamFlag(
    isUnmappedQuery=FALSE,
    isDuplicate=FALSE,
    isNotPassingQualityControls=FALSE
  ),
  simpleCigar = FALSE,
  reverseComplement = FALSE,
  what=c("qname","flag","rname","seq","strand","pos","qwidth","cigar","qual","mapq")
)  ### NOTE isValidVendorRead=FALSE should be TRUE

param.pile <- PileupParam(
  max_depth=2500,
  min_base_quality=0,
  min_mapq=0,
  min_nucleotide_depth=1,
  min_minor_allele_depth=0,
  distinguish_strands=TRUE,
  distinguish_nucleotides=TRUE,
  ignore_query_Ns=TRUE,
  include_deletions=TRUE,
  cycle_bins=numeric()
)