java -jar picard.jar CollectSequencingArtifactMetrics I=input.bamO=artifact_metrics.txtR=reference_sequence.fasta
INTERVALS (File) An optional list of intervals to restrict analysis to. Default value: null.
DB_SNP (File) VCF format dbSNP file, used to exclude regions around known polymorphisms from analysis. Default value: null.
MINIMUM_QUALITY_SCORE (Integer) The minimum base quality score for a base to be included in analysis. Default value: 20. This option can be set to 'null' to clear the default value.
MINIMUM_MAPPING_QUALITY (Integer) The minimum mapping quality score for a base to be included in analysis. Default value: 30. This option can be set to 'null' to clear the default value.
MINIMUM_INSERT_SIZE (Integer) The minimum insert size for a read to be included in analysis. Default value: 60. This option can be set to 'null' to clear the default value.
MAXIMUM_INSERT_SIZE (Integer) The maximum insert size for a read to be included in analysis. Set to 0 to have no maximum. Default value: 600. This option can be set to 'null' to clear the default value.
INCLUDE_UNPAIRED (Boolean) Include unpaired reads. If set to true then all paired reads will be included as well - MINIMUM_INSERT_SIZE and MAXIMUM_INSERT_SIZE will be ignored. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
INCLUDE_DUPLICATES (Boolean) Include duplicate reads. If set to true then all reads flagged as duplicates will be included as well. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
INCLUDE_NON_PF_READS (Boolean) Whether or not to include non-PF reads. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
TANDEM_READS (Boolean) Set to true if mate pairs are being sequenced from the same strand, i.e. they're expected to face the same direction. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
USE_OQ (Boolean) When available, use original quality scores for filtering. Default value: true. This option can be set to 'null' to clear the default value. Possible values: {true, false}
CONTEXT_SIZE (Integer) The number of context bases to include on each side of the assayed base. Default value: 1. This option can be set to 'null' to clear the default value.
CONTEXTS_TO_PRINT (String) If specified, only print results for these contexts in the detail metrics output. However, the summary metrics output will still take all contexts into consideration. Default value: null. This option may be specified 0 or more times.
FILE_EXTENSION (String) Append the given file extension to all metric file names (ex. OUTPUT.pre_adapter_summary_metrics.EXT). None if null Default value: null.
INPUT (File) Input SAM or BAM file. Required.
OUTPUT (File) File to write the output to. Required.
ASSUME_SORTED (Boolean) If true (default), then the sort order in the header file will be ignored. Default value: true. This option can be set to 'null' to clear the default value. Possible values: {true, false}
STOP_AFTER (Long) Stop after processing N reads, mainly for debugging. Default value: 0. This option can be set to 'null' to clear the default value.