dupBam: Duplicates operation in bam

In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

Duplicates operation in bam

Description

Mark or remove the duplicates in bam file.

Usage

  dupBam(inBam, outBam, operation=c("mark", "remove"))

Arguments

inBam	character(1): the input bam file.
outBam	character(1): the output bam file.
operation	character(1): either to mark or remove the duplicates in bam file.

Details

It use “sambamba” to mark and remove the duplicates, as the same criteria of “picard”.

Other alternatives are “samtools” with ‘fixmate’ and ‘markdup’, “picard”'s ‘MarkDuplicates’.

Value

invisible outBam file.

Author(s)

Ge Tan

Examples

  bamFile <- system.file("extdata", "ex1.bam", package="Rsamtools",
                         mustWork=TRUE)
  outBam <- tempfile(pattern="test-", fileext=".bam")
  dupBam(inBam=bamFile, outBam=outBam, operation="mark")
  dupBam(inBam=bamFile, outBam=outBam, operation="remove")

uzh/ezRun documentation built on Dec. 26, 2024, 9:53 a.m.