java -jar picard.jar CollectJumpingLibraryMetrics I=input.bam O=jumping_metrics.txt
INPUT (File) BAM file(s) of reads with duplicates marked Default value: null. This option may be specified 0 or more times.
OUTPUT (File) File to which metrics should be written Required.
MINIMUM_MAPPING_QUALITY (Integer) Mapping quality minimum cutoff Default value: 0. This option can be set to 'null' to clear the default value.
TAIL_LIMIT (Integer) When calculating mean and stdev stop when the bins in the tail of the distribution contain fewer than mode/TAIL_LIMIT items Default value: 10000. This option can be set to 'null' to clear the default value.
CHIMERA_KB_MIN (Integer) Jumps greater than or equal to the greater of this value or 2 times the mode of the outward-facing pairs are considered chimeras Default value: 100000. This option can be set to 'null' to clear the default value.