Takes a SAM or BAM file and separates all the reads into one SAM or BAM file per library name. Reads that do not have a read group specified or whose read group does not have a library name are written to a file called 'unknown.' The format (SAM or BAM) of the output files matches that of the input file.
java -jar picard.jar SplitSamByLibrary
INPUT (File) The SAM or BAM file to be split. Required.
OUTPUT (File) The directory where the library SAM or BAM files should be written (defaults to the current directory). Default value: /home/jcarey/picard/.. This option can be set to 'null' to clear the default value.