View source: R/markDuplicates.R
picardMarkDuplicates | R Documentation |
picardMarkDuplicates
Mark duplicated reads from a BAM file by calling
picard tools
picardMarkDuplicates(bam, out, path, verbose, threads = 1, maxmem = "4g")
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 |
This function is supposed to be called through the markDuplicates
wrapper
The return code of the system call
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