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. For each PROGRAM, the tool produces outputs. The valid values for PROGRAM and the output that would be generated by it are listed in the documentation of the PROGRAM argument.
Currently all programs are run with default options and fixed output extensions, but this may become more flexible in future. Specifying a reference sequence file is required.
Note: Metrics labeled as percentages (PCT_*) are actually expressed as fractions!
Usage example (all modules on by default):
java -jar picard.jar CollectMultipleMetrics \
I=input.bam \
O=multiple_metrics \
R=reference_sequence.fasta
Usage example (two modules only):
java -jar picard.jar CollectMultipleMetrics \I=input.bam \
O=multiple_metrics \
R=reference_sequence.fasta \
PROGRAM=null \
PROGRAM=QualityScoreDistribution \
PROGRAM=MeanQualityByCycle
Category Diagnostics and Quality Control
Overview
Class that is designed to instantiate and execute multiple metrics programs that extend SinglePassSamProgram while making only a single pass through the SAM file and supplying each program with the records as it goes.CollectMultipleMetrics (Picard) specific arguments
This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.
Argument name(s) | Default value | Summary | |
---|---|---|---|
Required Arguments | |||
--INPUT -I |
Input SAM or BAM file. | ||
--OUTPUT -O |
Base name of output files. | ||
Optional Tool Arguments | |||
--arguments_file |
read one or more arguments files and add them to the command line | ||
--ASSUME_SORTED -AS |
true | If true (default), then the sort order in the header file will be ignored. | |
--DB_SNP |
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. | ||
--EXTRA_ARGUMENT |
extra arguments to the various tools can be specified using the following format::: where is one of the programs specified in PROGRAM, and are the argument and value that you'd like to specify as you would on the command line. For example, to change the HISTOGRAM_WIDTH in CollectInsertSizeMetrics to 200, use: "EXTRA_ARGUMENT=CollectInsertSizeMetrics::HISTOGRAM_WIDTH=200" or, in the new parser:--EXTRA_ARGUMENT "CollectInsertSizeMetrics::--HISTOGRAM_WIDTH 200" (Quotes are required to avoid the shell from separating this into two arguments.) Note that the following arguments cannot be modified on a per-program level: INPUT, REFERENCE_SEQUENCE, ASSUME_SORTED, and STOP_AFTER. Providing them in an EXTRA_ARGUMENT will _not_ result in an error, but they will be silently ignored. | ||
--FILE_EXTENSION -EXT |
Append the given file extension to all metric file names (ex. OUTPUT.insert_size_metrics.EXT). None if null | ||
--help -h |
false | display the help message | |
--IGNORE_SEQUENCE |
If a read maps to a sequence specified with this option, all the bases in the read are counted as ignored bases. | ||
--INCLUDE_UNPAIRED -UNPAIRED |
false | 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. | |
--INTERVALS |
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. | ||
--METRIC_ACCUMULATION_LEVEL -LEVEL |
[ALL_READS] | The level(s) at which to accumulate metrics. | |
--PROGRAM |
[CollectAlignmentSummaryMetrics, CollectBaseDistributionByCycle, CollectInsertSizeMetrics, MeanQualityByCycle, QualityScoreDistribution] | Set of metrics programs to apply during the pass through the SAM file. | |
--REF_FLAT |
Gene annotations in refFlat form. Format described here: http://genome.ucsc.edu/goldenPath/gbdDescriptionsOld.html#RefFlat | ||
--STOP_AFTER |
0 | Stop after processing N reads, mainly for debugging. | |
--version |
false | display the version number for this tool | |
Optional Common Arguments | |||
--COMPRESSION_LEVEL |
5 | Compression level for all compressed files created (e.g. BAM and VCF). | |
--CREATE_INDEX |
false | Whether to create an index when writing VCF or coordinate sorted BAM output. | |
--CREATE_MD5_FILE |
false | Whether to create an MD5 digest for any BAM or FASTQ files created. | |
--GA4GH_CLIENT_SECRETS |
client_secrets.json | Google Genomics API client_secrets.json file path. | |
--MAX_RECORDS_IN_RAM |
500000 | When writing files that need to be sorted, this will specify the number of records stored in RAM before spilling to disk. Increasing this number reduces the number of file handles needed to sort the file, and increases the amount of RAM needed. | |
--QUIET |
false | Whether to suppress job-summary info on System.err. | |
--REFERENCE_SEQUENCE -R |
Reference sequence file. | ||
--TMP_DIR |
One or more directories with space available to be used by this program for temporary storage of working files | ||
--USE_JDK_DEFLATER -use_jdk_deflater |
false | Use the JDK Deflater instead of the Intel Deflater for writing compressed output | |
--USE_JDK_INFLATER -use_jdk_inflater |
false | Use the JDK Inflater instead of the Intel Inflater for reading compressed input | |
--VALIDATION_STRINGENCY |
STRICT | Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded. | |
--VERBOSITY |
INFO | Control verbosity of logging. | |
Advanced Arguments | |||
--showHidden |
false | display hidden arguments |
Argument details
Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.
--arguments_file
read one or more arguments files and add them to the command line
List[File] []
--ASSUME_SORTED / -AS
If true (default), then the sort order in the header file will be ignored.
boolean true
--COMPRESSION_LEVEL
Compression level for all compressed files created (e.g. BAM and VCF).
int 5 [ [ -∞ ∞ ] ]
--CREATE_INDEX
Whether to create an index when writing VCF or coordinate sorted BAM output.
Boolean false
--CREATE_MD5_FILE
Whether to create an MD5 digest for any BAM or FASTQ files created.
boolean false
--DB_SNP
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.
File null
--EXTRA_ARGUMENT
extra arguments to the various tools can be specified using the following format::: where is one of the programs specified in PROGRAM, and are the argument and value that you'd like to specify as you would on the command line. For example, to change the HISTOGRAM_WIDTH in CollectInsertSizeMetrics to 200, use:
"EXTRA_ARGUMENT=CollectInsertSizeMetrics::HISTOGRAM_WIDTH=200"
or, in the new parser:--EXTRA_ARGUMENT "CollectInsertSizeMetrics::--HISTOGRAM_WIDTH 200"
(Quotes are required to avoid the shell from separating this into two arguments.) Note that the following arguments cannot be modified on a per-program level: INPUT, REFERENCE_SEQUENCE, ASSUME_SORTED, and STOP_AFTER. Providing them in an EXTRA_ARGUMENT will _not_ result in an error, but they will be silently ignored.
List[String] []
--FILE_EXTENSION / -EXT
Append the given file extension to all metric file names (ex. OUTPUT.insert_size_metrics.EXT). None if null
String null
--GA4GH_CLIENT_SECRETS
Google Genomics API client_secrets.json file path.
String client_secrets.json
--help / -h
display the help message
boolean false
--IGNORE_SEQUENCE
If a read maps to a sequence specified with this option, all the bases in the read are counted as ignored bases.
Set[String] []
--INCLUDE_UNPAIRED / -UNPAIRED
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.
boolean false
--INPUT / -I
Input SAM or BAM file.
R File null
--INTERVALS
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.
File null
--MAX_RECORDS_IN_RAM
When writing files that need to be sorted, this will specify the number of records stored in RAM before spilling to disk. Increasing this number reduces the number of file handles needed to sort the file, and increases the amount of RAM needed.
Integer 500000 [ [ -∞ ∞ ] ]
--METRIC_ACCUMULATION_LEVEL / -LEVEL
The level(s) at which to accumulate metrics.
The --METRIC_ACCUMULATION_LEVEL argument is an enumerated type (Set[MetricAccumulationLevel]), which can have one of the following values:
- ALL_READS
- SAMPLE
- LIBRARY
- READ_GROUP
Set[MetricAccumulationLevel] [ALL_READS]
--OUTPUT / -O
Base name of output files.
R String null
--PROGRAM
Set of metrics programs to apply during the pass through the SAM file.
The --PROGRAM argument is an enumerated type (Set[Program]), which can have one of the following values:
- CollectAlignmentSummaryMetrics
- Produces a summary of alignment metrics from a SAM or BAM file. Creates output with ".alignment_summary_metrics, .read_length_histogram.pdf" appended to OUTPUT.
- CollectInsertSizeMetrics
- Collect metrics about the insert size distribution of a paired-end library. Creates output with ".insert_size_metrics, .insert_size_histogram.pdf" appended to OUTPUT.
- QualityScoreDistribution
- Chart the distribution of quality scores. Creates output with ".quality_distribution_metrics, .quality_distribution.pdf" appended to OUTPUT.
- MeanQualityByCycle
- Collect mean quality by cycle.Creates output with ".quality_by_cycle_metrics, .quality_by_cycle.pdf" appended to OUTPUT.
- CollectBaseDistributionByCycle
- Chart the nucleotide distribution per cycle in a SAM or BAM fileCreates output with ".base_distribution_by_cycle_metrics, .base_distribution_by_cycle.pdf" appended to OUTPUT.
- CollectGcBiasMetrics
- Collect metrics regarding GC bias. Creates output with ".gc_bias.detail_metrics, .gc_bias.summary_metrics, .gc_bias.pdf" appended to OUTPUT.
- RnaSeqMetrics
- Produces RNA alignment metrics for a SAM or BAM file. Creates output with ".rna_metrics, .rna_coverage.pdf" appended to OUTPUT.
- CollectSequencingArtifactMetrics
- Collect metrics to quantify single-base sequencing artifacts. Creates output with ".bait_bias_detail_metrics, .bait_bias_summary_metrics, .pre_adapter_detail_metrics, .pre_adapter_summary_metrics, .error_summary_metrics" appended to OUTPUT.
- CollectQualityYieldMetrics
- Collect metrics about reads that pass quality thresholds and Illumina-specific filters. Creates output with ".quality_yield_metrics" appended to OUTPUT.
Set[Program] [CollectAlignmentSummaryMetrics, CollectBaseDistributionByCycle, CollectInsertSizeMetrics, MeanQualityByCycle, QualityScoreDistribution]
--QUIET
Whether to suppress job-summary info on System.err.
Boolean false
--REF_FLAT
Gene annotations in refFlat form. Format described here: http://genome.ucsc.edu/goldenPath/gbdDescriptionsOld.html#RefFlat
File null
--REFERENCE_SEQUENCE / -R
Reference sequence file.
File null
--showHidden / -showHidden
display hidden arguments
boolean false
--STOP_AFTER
Stop after processing N reads, mainly for debugging.
int 0 [ [ -∞ ∞ ] ]
--TMP_DIR
One or more directories with space available to be used by this program for temporary storage of working files
List[File] []
--USE_JDK_DEFLATER / -use_jdk_deflater
Use the JDK Deflater instead of the Intel Deflater for writing compressed output
Boolean false
--USE_JDK_INFLATER / -use_jdk_inflater
Use the JDK Inflater instead of the Intel Inflater for reading compressed input
Boolean false
--VALIDATION_STRINGENCY
Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.
The --VALIDATION_STRINGENCY argument is an enumerated type (ValidationStringency), which can have one of the following values:
- STRICT
- LENIENT
- SILENT
ValidationStringency STRICT
--VERBOSITY
Control verbosity of logging.
The --VERBOSITY argument is an enumerated type (LogLevel), which can have one of the following values:
- ERROR
- WARNING
- INFO
- DEBUG
LogLevel INFO
--version
display the version number for this tool
boolean false
GATK version 4.2.4.0-SNAPSHOT built at Thu, 16 Dec 2021 11:57:48 -0800.
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