Package picard.sam.markduplicates
package picard.sam.markduplicates
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ClassDescriptionCollect DuplicateMark'ing metrics from an input file that was already Duplicate-Marked.Attempts to estimate library complexity from sequence alone.A better duplication marking algorithm that handles all cases including clipped and gapped alignments.Enum used to control how duplicates are flagged in the DT optional tag on each read.Enum for the possible values that a duplicate read can be tagged with in the DT attribute.MarkDuplicates calculation helper class for flow based mode The class extends the behavior of MarkDuplicates which contains the complete code for the non-flow based mode.An even better duplication marking algorithm that handles all cases including clipped and gapped alignments.This will iterate through a coordinate sorted SAM file (iterator) and either mark or remove duplicates as appropriate.This is a simple tool to mark duplicates using the DuplicateSetIterator, DuplicateSet, and SAMRecordDuplicateComparator.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 is used to identify UMIs that come from the same original source molecule.Metrics that are calculated during the process of marking duplicates within a stream of SAMRecords using the UmiAwareDuplicateSetIterator.