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JumpingLibraryMetrics Follow

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GATK Team
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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.

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GATK version 4.6.0.0-33-gdffedfb built at Wed, 23 Oct 2024 21:44:48 -0400.

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