Mark duplicates using bamutil

bamutilMarkDuplicates Mark duplicated reads from a BAM file by calling bamutil

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