bamutilMarkDuplicates: Mark duplicates using bamutil

In ssayols/dupRadar: Assessment of duplication rates in RNA-Seq datasets

Mark duplicates using bamutil

Description

bamutilMarkDuplicates Mark duplicated reads from a BAM file by calling bamutil

Usage

bamutilMarkDuplicates(bam, out, path, verbose)

Arguments

bam	The bam file to mark duplicates from
out	Regular expression describing the transformation on the original filename to get the output filename. By default, a "_duprm" suffix is added before the bam extension
path	Path to the duplicate marker binaries
verbose	Redirect all the program output to the R console

Details

This function is supposed to be called through the markDuplicates wrapper

Value

The return code of the system call

ssayols/dupRadar documentation built on Oct. 10, 2023, 10:18 p.m.