With this option is it required that the BARCODE_TAG hold non-normalized UMIs. All chimeric reads and read fragments are treated as having come from the top strand. Both reads from a read pair considered top strand if the read 1 unclipped 5' coordinate is less than the read 2 unclipped 5' coordinate. A UMI from the 'top' strand is already normalized as it is. A UMI from the 'bottom' strand is normalized by swapping its content around the hyphen (eg. Reads are considered duplicates if, in addition to standard definition, have identical normalized UMIs. This option requires that the UMI consist of two equal length strings that are separated by a hyphen (e.g. Default trueĬomment(s) to include in the output file's header. Should be set to false if input SAM doesn't have this tag. BC for 10X Genomics)Ĭlear DT tag from input SAM records. If not null, assume that the input file has this order even if the header says otherwise.īarcode SAM tag (ex. Read one or more arguments files and add them to the command line The output file to write marked records to One or more input SAM or BAM files to analyze. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list. This table summarizes the command-line arguments that are specific to this tool. MarkDuplicates (Picard) specific arguments M=marked_dup_metrics.txtPlease see MarkDuplicates for detailed explanations of the output metrics.Ī better duplication marking algorithm that handles all cases including clipped Usage example: java -jar picard.jar MarkDuplicates \ If desired, duplicates can be removed using the REMOVE_DUPLICATE and REMOVE_SEQUENCING_DUPLICATES options. However, when the input is query-sorted (actually query-grouped), then unmapped mates and secondary/supplementary reads are not excluded from the duplication test and can be marked as duplicate reads. When 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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