bamutilMarkDuplicates: Mark duplicates using bamutil

Description Usage Arguments Details Value

View source: R/markDuplicates.R

Description

bamutilMarkDuplicates Mark duplicated reads from a BAM file by calling bamutil

Usage

1
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


Bioconductor-mirror/dupRadar documentation built on June 1, 2017, 7:37 a.m.