Sam/Bam Manipulation


java -jar picard.jar CollectIlluminaBasecallingMetrics BASECALLS_DIR=/BaseCalls/ LANE=001 READ_STRUCTURE=25T8B25T INPUT=barcode_list.txt


BASECALLS_DIR (File)    The Illumina basecalls output directory from which data are read Required.
BARCODES_DIR (File)    The barcodes directory with _barcode.txt files (generated by ExtractIlluminaBarcodes). If not set, use BASECALLS_DIR. Default value: null.
LANE (Integer)    The lane whose data will be read Required.
INPUT (File)    The file containing barcodes to expect from the run - barcodeData.# Default value: null.
READ_STRUCTURE (String)    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: * read one with 28 cycles (bases) of template * read two with 8 cycles (bases) of molecular barcode (ex. unique molecular barcode) * read three with 8 cycles (bases) of sample barcode * 8 cycles (bases) skipped. * read four with 28 cycles (bases) of template The skipped cycles would NOT be included in an output SAM/BAM file or in read groups therein. Required.
OUTPUT (File)    The file to which the collected metrics are written Default value: null.

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