bamutilMarkDuplicates: 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
Value
The return code of the system call
Details
This function is supposed to be called through the markDuplicates
wrapper