DuplicationMetrics – GATK

Metrics

Overview

Metrics that are calculated during the process of marking duplicates within a stream of SAMRecords.

This table summarizes the values that are specific to this metric.

Metric	Summary
LIBRARY	The library on which the duplicate marking was performed.
UNPAIRED_READS_EXAMINED	The number of mapped reads examined which did not have a mapped mate pair, either because the read is unpaired, or the read is paired to an unmapped mate.
READ_PAIRS_EXAMINED	The number of mapped read pairs examined. (Primary, non-supplemental)
SECONDARY_OR_SUPPLEMENTARY_RDS	The number of reads that were either secondary or supplementary
UNMAPPED_READS	The total number of unmapped reads examined. (Primary, non-supplemental)
UNPAIRED_READ_DUPLICATES	The number of fragments that were marked as duplicates.
READ_PAIR_DUPLICATES	The number of read pairs that were marked as duplicates.
READ_PAIR_OPTICAL_DUPLICATES	The number of read pairs duplicates that were caused by optical duplication. Value is always < READ_PAIR_DUPLICATES, which counts all duplicates regardless of source.
PERCENT_DUPLICATION	The fraction of mapped sequence that is marked as duplicate.
ESTIMATED_LIBRARY_SIZE	The estimated number of unique molecules in the library based on PE duplication.

GATK version 4.6.0.0 built at Sat, 29 Jun 2024 20:47:29 -0400.