Class CollectTargetedPcrMetrics
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.analysis.directed.CollectTargetedMetrics<TargetedPcrMetrics,TargetedPcrMetricsCollector>
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- picard.analysis.directed.CollectTargetedPcrMetrics
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@DocumentedFeature public class CollectTargetedPcrMetrics extends CollectTargetedMetrics<TargetedPcrMetrics,TargetedPcrMetricsCollector>
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_listTargetedPcrMetrics
for detailed explanations of the output metrics produced by this tool.
Collect metric information for target pcr metrics runs. SeeCollectTargetedMetrics
andTargetedPcrMetricsCollector
for more information
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Field Summary
Fields Modifier and Type Field Description File
AMPLICON_INTERVALS
String
CUSTOM_AMPLICON_SET_NAME
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Fields 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
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Fields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, 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 Constructor Description CollectTargetedPcrMetrics()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected htsjdk.samtools.util.IntervalList
getProbeIntervals()
protected String
getProbeSetName()
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
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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 Detail
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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
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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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Method Detail
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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
protected String 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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