Description

Collect jumping library metrics. This tool collects high-level metrics about the presence of outward-facing (jumping) and inward-facing (non-jumping) read pairs within a SAM or BAM file. For a brief primer on jumping libraries, see the GATK Dictionary. This program gets all data for computation from the first read in each pair in which the mapping quality (MQ) tag is set with the mate's mapping quality. If the MQ tag is not set, then the program assumes that the mate's MQ is greater than or equal to MINIMUM_MAPPING_QUALITY (default value is 0). Note: Metrics labeled as percentages are actually expressed as fractions!