picard.analysis.directed

Class CollectTargetedPcrMetrics

java.lang.Object

picard.cmdline.CommandLineProgram

picard.analysis.directed.CollectTargetedMetrics<TargetedPcrMetrics,TargetedPcrMetricsCollector>

picard.analysis.directed.CollectTargetedPcrMetrics

@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 \\

      I=input.bam \\

      O=output_pcr_metrics.txt \\

      R=reference.fasta \\

      AMPLICON_INTERVALS=amplicon.interval_list \\

      TARGET_INTERVALS=targets.interval_list
 

Please see the metrics definitions page on 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

Fields

Modifier and Type	Field and Description
java.io.File	AMPLICON_INTERVALS
java.lang.String	CUSTOM_AMPLICON_SET_NAME

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

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, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

Constructors

Constructor and Description
CollectTargetedPcrMetrics()

Method Summary

Modifier and Type	Method and Description
protected htsjdk.samtools.util.IntervalList	getProbeIntervals()
protected java.lang.String	getProbeSetName()
protected TargetedPcrMetricsCollector	makeCollector(java.util.Set<MetricAccumulationLevel> accumulationLevels, java.util.List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords, htsjdk.samtools.reference.ReferenceSequenceFile refFile, java.io.File perTargetCoverage, java.io.File perBaseCoverage, htsjdk.samtools.util.IntervalList targetIntervals, htsjdk.samtools.util.IntervalList probeIntervals, java.lang.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

getCommandLine, getCommandLineParser, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

AMPLICON_INTERVALS

@Argument(shortName="AI",
          doc="An interval list file that contains the locations of the baits used.")
public java.io.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 java.lang.String CUSTOM_AMPLICON_SET_NAME

Constructor Detail

CollectTargetedPcrMetrics

public CollectTargetedPcrMetrics()

Method Detail

getProbeIntervals

protected htsjdk.samtools.util.IntervalList getProbeIntervals()

Specified by:

getProbeIntervals in class CollectTargetedMetrics<TargetedPcrMetrics,TargetedPcrMetricsCollector>

Returns:

AMPLICON_INTERVALS

getProbeSetName

protected java.lang.String getProbeSetName()

Specified by:

getProbeSetName in class CollectTargetedMetrics<TargetedPcrMetrics,TargetedPcrMetricsCollector>

Returns:

CUSTOM_AMPLICON_SET_NAME

makeCollector

protected TargetedPcrMetricsCollector makeCollector(java.util.Set<MetricAccumulationLevel> accumulationLevels,
                                                    java.util.List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords,
                                                    htsjdk.samtools.reference.ReferenceSequenceFile refFile,
                                                    java.io.File perTargetCoverage,
                                                    java.io.File perBaseCoverage,
                                                    htsjdk.samtools.util.IntervalList targetIntervals,
                                                    htsjdk.samtools.util.IntervalList probeIntervals,
                                                    java.lang.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 class CollectTargetedMetrics<TargetedPcrMetrics,TargetedPcrMetricsCollector>

Returns:

A TargetMetricsCollector to which we will pass SAMRecords