Question: Pileup from Rsamtool missing snps in bam files
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gravatar for MAPK
4.9 years ago by
MAPK1.5k
United States
MAPK1.5k wrote:

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 shoudl 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() )
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ADD COMMENTlink modified 4.9 years ago • written 4.9 years ago by MAPK1.5k
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