Mark duplicates using Picard tools

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

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