Metrics
Category Metrics
Overview
High level metrics about the presence of outward- and inward-facing pairs within a SAM file generated with a jumping library, produced by the CollectJumpingLibraryMetrics program and usually stored in a file with the extension ".jump_metrics".This table summarizes the values that are specific to this metric.
| Metric | Summary |
|---|---|
| JUMP_PAIRS | The number of outward-facing pairs in the SAM file |
| JUMP_DUPLICATE_PAIRS | The number of outward-facing pairs that are duplicates |
| JUMP_DUPLICATE_PCT | The fraction of outward-facing pairs that are marked as duplicates |
| JUMP_LIBRARY_SIZE | The estimated library size for outward-facing pairs |
| JUMP_MEAN_INSERT_SIZE | The mean insert size for outward-facing pairs |
| JUMP_STDEV_INSERT_SIZE | The standard deviation on the insert size for outward-facing pairs |
| NONJUMP_PAIRS | The number of inward-facing pairs in the SAM file |
| NONJUMP_DUPLICATE_PAIRS | The number of inward-facing pais that are duplicates |
| NONJUMP_DUPLICATE_PCT | The fraction of inward-facing pairs that are marked as duplicates |
| NONJUMP_LIBRARY_SIZE | The estimated library size for inward-facing pairs |
| NONJUMP_MEAN_INSERT_SIZE | The mean insert size for inward-facing pairs |
| NONJUMP_STDEV_INSERT_SIZE | The standard deviation on the insert size for inward-facing pairs |
| CHIMERIC_PAIRS | The number of pairs where either (a) the ends fall on different chromosomes or (b) the insert size is greater than the maximum of 100000 or 2 times the mode of the insert size for outward-facing pairs. |
| FRAGMENTS | The number of fragments in the SAM file |
| PCT_JUMPS | The number of outward-facing pairs expressed as a fraction of the total of all outward facing pairs, inward-facing pairs, and chimeric pairs. |
| PCT_NONJUMPS | The number of inward-facing pairs expressed as a fraction of the total of all outward facing pairs, inward-facing pairs, and chimeric pairs. |
| PCT_CHIMERAS | The number of chimeric pairs expressed as a fraction of the total of all outward facing pairs, inward-facing pairs, and chimeric pairs. |
GATK version 4.5.0.0 built at Tue, 9 Jan 2024 14:37:17 -0500.
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