5/31/2023 0 Comments Duplicate detective smark markWhen the input is coordinate-sorted, unmapped mates of mapped records and supplementary/secondary alignments are not marked as duplicates. The program can take either coordinate-sorted or query-sorted inputs, however the behavior is slightly different. MarkDuplicates also produces a metrics file indicating the numbers of duplicates for both single- and paired-end reads. Note that without optical duplicate counts, library size estimation will be inaccurate. for RNA-seq or other data where duplicate sets are extremely large and estimating library complexity is not an aim. Set READ_NAME_REGEX to null to skip optical duplicate detection, e.g. This tool uses the READ_NAME_REGEX and the OPTICAL_DUPLICATE_PIXEL_DISTANCE options as the primary methods to identify and differentiate duplicate types. The records within the output of a SAM/BAM file will have values for the 'DT' tag (depending on the invoked TAGGING_POLICY), as either library/PCR-generated duplicates (LB), or sequencing-platform artifact duplicates (SQ). Invoking the TAGGING_POLICY option, you can instruct the program to mark all the duplicates (All), only the optical duplicates (OpticalOnly), or no duplicates (DontTag). To do this, a new tag called the duplicate type (DT) tag was recently added as an optional output in the 'optional field' section of a SAM/BAM file. If you are not familiar with this type of annotation, please see the following blog post for additional information.Īlthough the bitwise flag annotation indicates whether a read was marked as a duplicate, it does not identify the type of duplicate. Duplicates are marked with the hexadecimal value of 0x0400, which corresponds to a decimal value of 1024. The tool's main output is a new SAM or BAM file, in which duplicates have been identified in the SAM flags field for each read. After duplicate reads are collected, the tool differentiates the primary and duplicate reads using an algorithm that ranks reads by the sums of their base-quality scores (default method). An BARCODE_TAG option is available to facilitate duplicate marking using molecular barcodes. The MarkDuplicates tool works by comparing sequences in the 5 prime positions of both reads and read-pairs in a SAM/BAM file. These duplication artifacts are referred to as optical duplicates. Duplicate reads can also result from a single amplification cluster, incorrectly detected as multiple clusters by the optical sensor of the sequencing instrument. See also EstimateLibrar圜omplexity for additional notes on PCR duplication artifacts. Duplicates can arise during sample preparation e.g. 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.
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