Classify PF-Failing reads in a HiSeqX Illumina Basecalling directory into various categories.
java -jar picard.jar CollectHiSeqXPfFailMetrics BASECALLS_DIR=/BaseCalls/ OUTPUT=/metrics/ LANE=001
BASECALLS_DIR (File) The Illumina basecalls directory. Required.
OUTPUT (File) Basename for metrics file. Resulting file will be .pffail_summary_metrics Required.
PROB_EXPLICIT_READS (Double) The fraction of (non-PF) reads for which to output explicit classification. Output file will be .pffail_detailed_metrics (if PROB_EXPLICIT_READS != 0) Default value: 0.0. This option can be set to 'null' to clear the default value.
LANE (Integer) Lane number. Required.
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
N_CYCLES (Integer) Number of cycles to look at. At time of writing PF status gets determined at cycle 24 so numbers greater than this will yield strange results. In addition, PF status is currently determined at cycle 24, so running this with any other value is neither tested nor recommended. Default value: 24. This option can be set to 'null' to clear the default value.