java -jar picard.jar CollectTargetedPcrMetrics I=input.bam O=pcr_metrics.txt R=reference_sequence.fasta AMPLICON_INTERVALS=amplicon.interval_list TARGET_INTERVALS=targets.interval_list
AMPLICON_INTERVALS (File) An interval list file that contains the locations of the baits used. Required.
CUSTOM_AMPLICON_SET_NAME (String) Custom amplicon set name. If not provided it is inferred from the filename of the AMPLICON_INTERVALS intervals. Default value: null.
TARGET_INTERVALS (File) An interval list file that contains the locations of the targets. Default value: null. This option must be specified at least 1 times.
INPUT (File) An aligned SAM or BAM file. Required.
OUTPUT (File) The output file to write the metrics to. Required.
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.
PER_TARGET_COVERAGE (File) An optional file to output per target coverage information to. Default value: null.
PER_BASE_COVERAGE (File) An optional file to output per base coverage information to. The per-base file contains one line per target base and can grow very large. It is not recommended for use with large target sets. Default value: null.
NEAR_DISTANCE (Integer) The maximum distance between a read and the nearest probe/bait/amplicon for the read to be considered 'near probe' and included in percent selected. Default value: 250. This option can be set to 'null' to clear the default value.
MINIMUM_MAPPING_QUALITY (Integer) Minimum mapping quality for a read to contribute coverage. Default value: 1. This option can be set to 'null' to clear the default value.
MINIMUM_BASE_QUALITY (Integer) Minimum base quality for a base to contribute coverage. Default value: 0. This option can be set to 'null' to clear the default value.
CLIP_OVERLAPPING_READS (Boolean) True if we are to clip overlapping reads, false otherwise. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
COVERAGE_CAP (Integer) Parameter to set a max coverage limit for Theoretical Sensitivity calculations. Default is 200. Default value: 200. This option can be set to 'null' to clear the default value.
SAMPLE_SIZE (Integer) Sample Size used for Theoretical Het Sensitivity sampling. Default is 10000. Default value: 10000. This option can be set to 'null' to clear the default value.