DEPRECATED: Use CollectHsMetrics instead. Calculates a set of Hybrid Selection specific metrics from an aligned SAMor BAM file. If a reference sequence is provided, AT/GC dropout metrics will be calculated, and the PER_TARGET_COVERAGE option can be used to output GC and mean coverage information for every target.
java -jar picard.jar CalculateHsMetrics
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}
BAIT_INTERVALS (File) An interval list file that contains the locations of the baits used. Default value: null. This option must be specified at least 1 times.
BAIT_SET_NAME (String) Bait set name. If not provided it is inferred from the filename of the bait 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.
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.