| Class | Description |
|---|---|
| EstimateLibraryComplexity |
Attempts to estimate library complexity from sequence alone.
|
| MarkDuplicates |
A better duplication marking algorithm that handles all cases including clipped
and gapped alignments.
|
| MarkDuplicatesWithMateCigar |
An even better duplication marking algorithm that handles all cases including clipped
and gapped alignments.
|
| MarkDuplicatesWithMateCigarIterator |
This will iterate through a coordinate sorted SAM file (iterator) and either mark or
remove duplicates as appropriate.
|
| SimpleMarkDuplicatesWithMateCigar |
This is a simple tool to mark duplicates using the DuplicateSetIterator, DuplicateSet, and SAMRecordDuplicateComparator.
|
| UmiAwareMarkDuplicatesWithMateCigar |
This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads are
defined as originating from a single fragment of DNA.
|
| UmiGraph |
UmiGraph is used to identify UMIs that come from the same original source molecule.
|
| UmiMetrics |
Metrics that are calculated during the process of marking duplicates
within a stream of SAMRecords using the UmiAwareDuplicateSetIterator.
|
| Enum | Description |
|---|---|
| MarkDuplicates.DuplicateTaggingPolicy |
Enum used to control how duplicates are flagged in the DT optional tag on each read.
|
| MarkDuplicates.DuplicateType |
Enum for the possible values that a duplicate read can be tagged with in the DT attribute.
|