dupRadar (version 1.2.2)

picardMarkDuplicates: 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

Value

• The return code of the system call

Details

This function is supposed to be called through the markDuplicates wrapper