tally: Tally a genomic region

In Rariant: Identification and Assessment of Single Nucleotide Variants through Shifts in Non-Consensus Base Call Frequencies

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.

Details

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

Value

An integer array with the dimensions:

• positionLength: width(region)

• baseA, C, G, T

• strand+, -

See Also

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

Rariant documentation built on Nov. 8, 2020, 6:56 p.m.