tallyBam {Rariant} | R Documentation

## 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.

### 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

[Package Rariant version 1.25.0 Index]