### CalculateHsMetrics

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.

Option | Description
--- | ---
BAIT_INTERVALS=File | An interval list file that contains the locations of the baits used. Required.
TARGET_INTERVALS=File | An interval list file that contains the locations of the targets. Required.
INPUT=File | An aligned SAM or BAM file. Required.
OUTPUT=File | The output file to write the metrics to. Required. Cannot be used in conjuction with option(s) METRICS_FILE (M)
METRICS_FILE=File | Legacy synonym for OUTPUT, should not be used. Required. Cannot be used in conjuction with option(s) OUTPUT (O)
METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel | The level(s) at which to accumulate metrics. 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.
REFERENCE_SEQUENCE=File | The reference sequence aligned to. Default value: null.
PER_TARGET_COVERAGE=File | An optional file to output per target coverage information to. Default value: null.