bamQC {ATACseqQC} | R Documentation

## Mapping quality control

### Description

Check the mapping rate, PCR duplication rate, and mitochondria reads contamination.

### Usage

    bamQC(
      bamfile,
      index = bamfile,
      mitochondria = "chrM",
      outPath = sub(".bam", ".clean.bam", basename(bamfile)),
      doubleCheckDup = FALSE
    )

### Arguments

`bamfile` | character(1). File name of bam.
`index` | character(1). File name of index file.
`mitochondria` | character(1). Sequence name of mitochondria.
`outPath` | character(1). File name of cleaned bam.
`doubleCheckDup` | logical(1). Double check duplicates or not if there is no tags for that.

### Value

A list of quality summary.

### Author(s)

Jianhong Ou

### Examples

    bamfile <- system.file("extdata", "GL1.bam", package="ATACseqQC")
    bamQC(bamfile, outPath=NULL)

[Package ATACseqQC version 1.10.4 Index]