Class CollectIlluminaBasecallingMetrics

java.lang.Object
picard.cmdline.CommandLineProgram
picard.illumina.CollectIlluminaBasecallingMetrics

@DocumentedFeature public class CollectIlluminaBasecallingMetrics extends CommandLineProgram
A Command line tool to collect Illumina Basecalling metrics for a sequencing run Requires a Lane and an input file of Barcodes to expect. Outputs metrics:
  • Mean Clusters Per Tile
  • Standard Deviation of Clusters Per Tile
  • Mean Pf Clusters Per Tile
  • Standard Deviation of Pf Clusters Per Tile
  • Mean Percentage of Pf Clusters Per Tile
  • Standard Deviation of Percentage of Pf Clusters Per Tile
  • Field Details

    • BASECALLS_DIR

      @Argument(doc="The Illumina basecalls output directory from which data are read", shortName="B") public File BASECALLS_DIR
    • BARCODES_DIR

      @Argument(doc="The barcodes directory with _barcode.txt files (generated by ExtractIlluminaBarcodes). If not set, use BASECALLS_DIR. ", shortName="BCD", optional=true) public File BARCODES_DIR
    • LANE

      @Argument(doc="The lane whose data will be read", shortName="L") public Integer LANE
    • INPUT

      @Argument(doc="The file containing barcodes to expect from the run - barcodeData.#", shortName="I", optional=true) public File INPUT
    • READ_STRUCTURE

      @Argument(doc="A description of the logical structure of clusters in an Illumina Run, i.e. a description of the structure IlluminaBasecallsToSam assumes the data to be in. It should consist of integer/character pairs describing the number of cycles and the type of those cycles (B for Sample Barcode, M for molecular barcode, T for Template, and S for skip). E.g. If the input data consists of 80 base clusters and we provide a read structure of \"28T8M8B8S28T\" then the sequence may be split up into four reads:\n* read one with 28 cycles (bases) of template\n* read two with 8 cycles (bases) of molecular barcode (ex. unique molecular barcode)\n* read three with 8 cycles (bases) of sample barcode\n* 8 cycles (bases) skipped.\n* read four with 28 cycles (bases) of template\nThe skipped cycles would NOT be included in an output SAM/BAM file or in read groups therein.", shortName="RS") public String READ_STRUCTURE
    • OUTPUT

      @Argument(doc="The file to which the collected metrics are written", shortName="O", optional=true) public File OUTPUT
  • Constructor Details

    • CollectIlluminaBasecallingMetrics

      public CollectIlluminaBasecallingMetrics()
  • Method Details

    • doWork

      protected int doWork()
      Description copied from class: CommandLineProgram
      Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.
      Specified by:
      doWork in class CommandLineProgram
      Returns:
      program exit status.