Collects metrics from reduced representation bisulfite sequencing (Rrbs) data.
java -jar picard.jar CollectRrbsMetrics R=reference_sequence.fasta I=input.bam M=basename_for_metrics_files
INPUT (File) The BAM or SAM file containing aligned reads. Must be coordinate sorted Required.
METRICS_FILE_PREFIX (String) Base name for output files Required.
REFERENCE (File) The reference sequence fasta file Required.
MINIMUM_READ_LENGTH (Integer) Minimum read length Default value: 5. This option can be set to 'null' to clear the default value.
C_QUALITY_THRESHOLD (Integer) Threshold for base quality of a C base before it is considered Default value: 20. This option can be set to 'null' to clear the default value.
NEXT_BASE_QUALITY_THRESHOLD (Integer) Threshold for quality of a base next to a C before the C base is considered Default value: 10. This option can be set to 'null' to clear the default value.
MAX_MISMATCH_RATE (Double) Maximum percentage of mismatches in a read for it to be considered, with a range of 0-1 Default value: 0.1. This option can be set to 'null' to clear the default value.
SEQUENCE_NAMES (String) Set of sequence names to consider, if not specified all sequences will be used Default value: null. This option may be specified 0 or more times.
ASSUME_SORTED (Boolean) If true, assume that the input file is coordinate sorted even if the header says otherwise. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
METRIC_ACCUMULATION_LEVEL (MetricAccumulationLevel) The level(s) at which to accumulate metrics. Default value: [ALL_READS]. This option can be set to 'null' to clear the default value. Possible values: {ALL_READS, SAMPLE, LIBRARY, READ_GROUP} This option may be specified 0 or more times. This option can be set to 'null' to clear the default list.