Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments, but only at a set of sampled positions. It is important that the sampled positions be chosen so that they are spread out at least further than a read's length apart; otherwise, you run the risk of double-counting reads in the metrics. If contig-sized intervals are needed, use INTERVALS argument in CollectWgsMetrics.
java -jar picard.jar CollectWgsMetricsFromSampledSites
INTERVALS (File) An interval list file that contains the locations of the positions to assess. Required.
INPUT (File) Input SAM or BAM file. Required.
OUTPUT (File) Output metrics file. Required.
REFERENCE_SEQUENCE (File) The reference sequence fasta aligned to. Required.
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. N bases will be treated as having a base quality of negative infinity and will therefore be excluded from coverage regardless of the value of this parameter. Default value: 20. This option can be set to 'null' to clear the default value.
COVERAGE_CAP (Integer) Treat positions with coverage exceeding this value as if they had coverage at this value (but calculate the difference for PCT_EXC_CAPPED). Default value: 250. This option can be set to 'null' to clear the default value.
LOCUS_ACCUMULATION_CAP (Integer) At positions with coverage exceeding this value, completely ignore reads that accumulate beyond this value (so that they will not be considered for PCT_EXC_CAPPED). Used to keep memory consumption in check, but could create bias if set too low Default value: 100000. This option can be set to 'null' to clear the default value.
STOP_AFTER (Long) For debugging purposes, stop after processing this many genomic bases. Default value: -1. This option can be set to 'null' to clear the default value.
INCLUDE_BQ_HISTOGRAM (Boolean) Determines whether to include the base quality histogram in the metrics file. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
COUNT_UNPAIRED (Boolean) If true, count unpaired reads, and paired reads with one end unmapped Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
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.