Rariant (version 1.8.3)

tallyBam: Tally a genomic region

Description

Create the nucleotide count table ('tally') of a genomic region from a BAM file.

Usage

tallyBamRegion(bam, region, minBase = 0, minMap = 0, maxDepth = 10000)

Arguments

bam

BAM file

region

GRanges with the region to tally, with one entry.

minBase, minMap

Minimum base call and mapping quality for reads to be considered for the nucleotide count table [default: 0]. Reads with a lower quality are dropped.

maxDepth

Maximal sequencing depth to analyze.

Value

• An integer array with the dimensions:
  • position
  {Length: width(region)}

• base
  A, C, G, T
• strand
  +, -

Details

For details, look at the documentation of the underlying 'tallyBAM' function in the 'h5vc' package.

See Also

h5vc::tallyBAM, deepSNV::bam2R, Rsamtools::pileup