Collects Illumina lane metrics for the given BaseCalling analysis directory. This tool produces quality control metrics on cluster density for each lane of an Illumina flowcell. This tool takes Illumina TileMetrics data and places them into directories containing lane- and phasing-level metrics. In this context, phasing refers to the fraction of molecules that fall behind or jump ahead (prephasing) during a read cycle.
java -jar picard.jar CollectIlluminaLaneMetrics RUN_DIR=test_run OUTPUT_DIRECTORY=Lane_output_metrics OUTPUT_PREFIX=experiment1 READ_STRUCTURE=25T8B25T
RUN_DIRECTORY (File) The Illumina run directory of the run for which the lane metrics are to be generated Required.
OUTPUT_DIRECTORY (File) The directory to which the output file will be written Required.
OUTPUT_PREFIX (String) The prefix to be prepended to the file name of the output file; an appropriate suffix will be applied Required.
READ_STRUCTURE (ReadStructure) 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.
If not given, will use the RunInfo.xml in the run directory. Default value: null.