Collect multiple classes of metrics. This 'meta-metrics' tool runs one or more of the metrics collection modules at the same time to cut down on the time spent reading in data from input files. Available modules include CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics, QualityScoreDistribution, MeanQualityByCycle, CollectBaseDistributionByCycle, CollectGcBiasMetrics, RnaSeqMetrics, CollectSequencingArtifactMetrics, and CollectQualityYieldMetrics. The tool produces outputs of '.pdf' and '.txt' files for each module, except for the CollectAlignmentSummaryMetrics module, which outputs only a '.txt' file. Output files are named by specifying a base name (without any file extensions).
java -jar picard.jar CollectMultipleMetrics I=input.bam O=multiple_metrics R=reference_sequence.fasta
INPUT (File) Input SAM or BAM file. 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 (Integer) Stop after processing N reads, mainly for debugging. Default value: 0. This option can be set to 'null' to clear the default value.
OUTPUT (String) Base name of output files. 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.
FILE_EXTENSION (String) Append the given file extension to all metric file names (ex. OUTPUT.insert_size_metrics.EXT). None if null Default value: null.
PROGRAM (Program) Set of metrics programs to apply during the pass through the SAM file. Default value: [CollectAlignmentSummaryMetrics, CollectBaseDistributionByCycle, CollectInsertSizeMetrics, MeanQualityByCycle, QualityScoreDistribution]. This option can be set to 'null' to clear the default value. Possible values: {CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics, QualityScoreDistribution, MeanQualityByCycle, CollectBaseDistributionByCycle, CollectGcBiasMetrics, RnaSeqMetrics, CollectSequencingArtifactMetrics, CollectQualityYieldMetrics} This option may be specified 0 or more times. This option can be set to 'null' to clear the default list.
INTERVALS (File) An optional list of intervals to restrict analysis to. Only pertains to some of the PROGRAMs. Programs whose stand-alone CLP does not have an INTERVALS argument will silently ignore this argument. Default value: null.
DB_SNP (File) VCF format dbSNP file, used to exclude regions around known polymorphisms from analysis by some PROGRAMs; PROGRAMs whose CLP doesn't allow for this argument will quietly ignore it. Default value: null.
INCLUDE_UNPAIRED (Boolean) Include unpaired reads in CollectSequencingArtifactMetrics. If set to true then all paired reads will be included as well - MINIMUM_INSERT_SIZE and MAXIMUM_INSERT_SIZE will be ignored in CollectSequencingArtifactMetrics. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}