picardMarkDuplicates: Mark duplicates using Picard tools

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

Mark duplicates using Picard tools

Description

picardMarkDuplicates Mark duplicated reads from a BAM file by calling picard tools

Usage

picardMarkDuplicates(bam, out, path, verbose, threads = 1, maxmem = "4g")

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
threads	Number of threads to use
maxmem	Max memory assigned to the jvm

Details

This function is supposed to be called through the markDuplicates wrapper

Value

The return code of the system call

imbforge/dupRadar documentation built on Oct. 18, 2023, 8:54 a.m.