Class CollectTargetedPcrMetrics
This tool calculates a set of PCR-related metrics from an aligned SAM or BAM file containing targeted sequencing data. It is appropriate for data produced with multiple small-target technologies including exome sequencing an custom amplicon panels such as the Illumina " + TruSeq Custom Amplicon (TSCA) kit.
If a reference sequence is provided, AT/GC dropout metrics will be calculated and the PER_TARGET_COVERAGE option can be used to output GC content and mean coverage information for each target. The AT/GC dropout metrics indicate the degree of inadequate coverage of a particular region based on its AT or GC content. The PER_TARGET_COVERAGE option can be used to output GC content and mean sequence depth information for every target interval.
Note: Metrics labeled as percentages are actually expressed as fractions!
Usage Example
java -jar picard.jar CollectTargetedPcrMetrics \\Please see the metrics definitions page on
I=input.bam \\
O=output_pcr_metrics.txt \\
R=reference.fasta \\
AMPLICON_INTERVALS=amplicon.interval_list \\
TARGET_INTERVALS=targets.interval_list
TargetedPcrMetrics
for detailed explanations of the output metrics produced by this tool.
Collect metric information for target pcr metrics runs. See
CollectTargetedMetrics
and TargetedPcrMetricsCollector
for
more information-
Field Summary
FieldsFields inherited from class picard.analysis.directed.CollectTargetedMetrics
ALLELE_FRACTION, CLIP_OVERLAPPING_READS, COVERAGE_CAP, INCLUDE_INDELS, INPUT, METRIC_ACCUMULATION_LEVEL, MINIMUM_BASE_QUALITY, MINIMUM_MAPPING_QUALITY, NEAR_DISTANCE, OUTPUT, PER_BASE_COVERAGE, PER_TARGET_COVERAGE, SAMPLE_SIZE, TARGET_INTERVALS, THEORETICAL_SENSITIVITY_OUTPUT
Fields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, SYNTAX_TRANSITION_URL, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected htsjdk.samtools.util.IntervalList
protected String
protected TargetedPcrMetricsCollector
makeCollector
(Set<MetricAccumulationLevel> accumulationLevels, List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords, htsjdk.samtools.reference.ReferenceSequenceFile refFile, File perTargetCoverage, File perBaseCoverage, htsjdk.samtools.util.IntervalList targetIntervals, htsjdk.samtools.util.IntervalList probeIntervals, String probeSetName, int nearProbeDistance) A factory method for the TargetMetricsCollector to use this time.Methods inherited from class picard.analysis.directed.CollectTargetedMetrics
customCommandLineValidation, doWork
Methods inherited from class picard.cmdline.CommandLineProgram
checkRInstallation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
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Field Details
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AMPLICON_INTERVALS
@Argument(shortName="AI", doc="An interval list file that contains the locations of the baits used.") public File AMPLICON_INTERVALS -
CUSTOM_AMPLICON_SET_NAME
@Argument(shortName="N", doc="Custom amplicon set name. If not provided it is inferred from the filename of the AMPLICON_INTERVALS intervals.", optional=true) public String CUSTOM_AMPLICON_SET_NAME
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Constructor Details
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CollectTargetedPcrMetrics
public CollectTargetedPcrMetrics()
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Method Details
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getProbeIntervals
protected htsjdk.samtools.util.IntervalList getProbeIntervals()- Specified by:
getProbeIntervals
in classCollectTargetedMetrics<TargetedPcrMetrics,
TargetedPcrMetricsCollector> - Returns:
- AMPLICON_INTERVALS
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getProbeSetName
- Specified by:
getProbeSetName
in classCollectTargetedMetrics<TargetedPcrMetrics,
TargetedPcrMetricsCollector> - Returns:
- CUSTOM_AMPLICON_SET_NAME
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makeCollector
protected TargetedPcrMetricsCollector makeCollector(Set<MetricAccumulationLevel> accumulationLevels, List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords, htsjdk.samtools.reference.ReferenceSequenceFile refFile, File perTargetCoverage, File perBaseCoverage, htsjdk.samtools.util.IntervalList targetIntervals, htsjdk.samtools.util.IntervalList probeIntervals, String probeSetName, int nearProbeDistance) Description copied from class:CollectTargetedMetrics
A factory method for the TargetMetricsCollector to use this time. Examples of TargetMetricsCollector: (TargetedPcrMetricsCollector, HsMetricsCalculator)- Specified by:
makeCollector
in classCollectTargetedMetrics<TargetedPcrMetrics,
TargetedPcrMetricsCollector> - Returns:
- A TargetMetricsCollector to which we will pass SAMRecords
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