Collects hybrid-selection (HS) metrics for a SAM or BAM file. This tool takes a SAM/BAM file input and collects metrics that are specific for sequence datasets generated through hybrid-selection. Hybrid-selection (HS) is the most commonly used technique to capture exon-specific sequences for targeted sequencing experiments such as exome sequencing; for more information, please see the corresponding GATK Dictionary entry.
java -jar picard.jar CollectHsMetrics I=input.bam O=hs_metrics.txt R=reference_sequence.fasta BAIT_INTERVALS=bait.interval_list TARGET_INTERVALS=target.interval_list
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.
MINIMUM_MAPPING_QUALITY (Integer) Minimum mapping quality for a read to contribute coverage. Default value: 20. 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: 20. 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: true. This option can be set to 'null' to clear the default value. Possible values: {true, false}
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.