@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!
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.
CollectTargetedMetrics and TargetedPcrMetricsCollector for
more information| Modifier and Type | Field | Description |
|---|---|---|
File |
AMPLICON_INTERVALS |
|
String |
CUSTOM_AMPLICON_SET_NAME |
CLIP_OVERLAPPING_READS, COVERAGE_CAP, INPUT, METRIC_ACCUMULATION_LEVEL, MINIMUM_BASE_QUALITY, MINIMUM_MAPPING_QUALITY, NEAR_DISTANCE, OUTPUT, PER_BASE_COVERAGE, PER_TARGET_COVERAGE, SAMPLE_SIZE, TARGET_INTERVALSCOMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY| Constructor | Description |
|---|---|
CollectTargetedPcrMetrics() |
| Modifier and Type | Method | Description |
|---|---|---|
protected htsjdk.samtools.util.IntervalList |
getProbeIntervals() |
|
protected String |
getProbeSetName() |
|
static void |
main(String[] argv) |
Stock main method.
|
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.
|
customCommandLineValidation, doWorkgetCommandLine, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser@Argument(shortName="AI",
doc="An interval list file that contains the locations of the baits used.")
public File AMPLICON_INTERVALS
@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
protected htsjdk.samtools.util.IntervalList getProbeIntervals()
getProbeIntervals in class CollectTargetedMetrics<TargetedPcrMetrics,TargetedPcrMetricsCollector>protected String getProbeSetName()
getProbeSetName in class CollectTargetedMetrics<TargetedPcrMetrics,TargetedPcrMetricsCollector>public static void main(String[] argv)
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)
CollectTargetedMetricsmakeCollector in class CollectTargetedMetrics<TargetedPcrMetrics,TargetedPcrMetricsCollector>