java -jar picard.jar ExtractIlluminaBarcodes BASECALLS_DIR=/BaseCalls/ LANE=1 READ_STRUCTURE=25T8B25T BARCODE_FILE=barcodes.txt METRICS_FILE=metrics_output.txt
BASECALLS_DIR (File) The Illumina basecalls directory. Required.
OUTPUT_DIR (File) Where to write _barcode.txt files. By default, these are written to BASECALLS_DIR. Default value: null.
LANE (Integer) Lane number. Required.
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.
BARCODE (String) Barcode sequence. These must be unique, and all the same length. This cannot be used with reads that have more than one barcode; use BARCODE_FILE in that case. Default value: null. This option may be specified 0 or more times. Cannot be used in conjuction with option(s) BARCODE_FILE
BARCODE_FILE (File) Tab-delimited file of barcode sequences, barcode name and, optionally, library name. Barcodes must be unique and all the same length. Column headers must be 'barcode_sequence_1', 'barcode_sequence_2' (optional), 'barcode_name', and 'library_name'. Required. Cannot be used in conjuction with option(s) BARCODE
METRICS_FILE (File) Per-barcode and per-lane metrics written to this file. Required.
MAX_MISMATCHES (Integer) Maximum mismatches for a barcode to be considered a match. Default value: 1. This option can be set to 'null' to clear the default value.
MIN_MISMATCH_DELTA (Integer) Minimum difference between number of mismatches in the best and second best barcodes for a barcode to be considered a match. Default value: 1. This option can be set to 'null' to clear the default value.
MAX_NO_CALLS (Integer) Maximum allowable number of no-calls in a barcode read before it is considered unmatchable. Default value: 2. This option can be set to 'null' to clear the default value.
MINIMUM_BASE_QUALITY (Integer) Minimum base quality. Any barcode bases falling below this quality will be considered a mismatch even in the bases match. Default value: 0. This option can be set to 'null' to clear the default value.
MINIMUM_QUALITY (Integer) The minimum quality (after transforming 0s to 1s) expected from reads. If qualities are lower than this value, an error is thrown.The default of 2 is what the Illumina's spec describes as the minimum, but in practice the value has been observed lower. Default value: 2. This option can be set to 'null' to clear the default value.
COMPRESS_OUTPUTS (Boolean) Compress output s_l_t_barcode.txt files using gzip and append a .gz extension to the file names. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
NUM_PROCESSORS (Integer) Run this many PerTileBarcodeExtractors in parallel. If NUM_PROCESSORS = 0, number of cores is automatically set to the number of cores available on the machine. If NUM_PROCESSORS