Constant Field Values
Contents
picard.analysis.*
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picard.analysis.CollectInsertSizeMetricsModifier and TypeConstant FieldValue
protected static final String
"picard/analysis/insertSizeHistogram.R"
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picard.analysis.CollectRrbsMetrics
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picard.analysis.artifacts.CollectSequencingArtifactMetricsModifier and TypeConstant FieldValue
public static final String
"Collect metrics to quantify single-base sequencing artifacts. "
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picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
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picard.analysis.artifacts.SequencingArtifactMetricsModifier and TypeConstant FieldValue
public static final String
".bait_bias_detail_metrics"
public static final String
".bait_bias_summary_metrics"
public static final String
".error_summary_metrics"
public static final String
".pre_adapter_detail_metrics"
public static final String
".pre_adapter_summary_metrics"
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picard.analysis.directed.RnaSeqMetricsCollector
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picard.analysis.directed.TargetMetricsCollector<METRIC_TYPE extends MultilevelMetrics>
picard.arrays.*
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picard.arrays.CreateBafRegressMetricsFile
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picard.arrays.CreateVerifyIDIntensityContaminationMetricsFile
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picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator
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picard.arrays.illumina.IlluminaManifestModifier and TypeConstant FieldValue
public static final String
"AddressA_ID"
public static final String
"AddressB_ID"
public static final String
"AlleleA_ProbeSeq"
public static final String
"AlleleB_ProbeSeq"
public static final String
"BeadSetID"
public static final String
"Chr"
public static final String
"Exp_Clusters"
public static final String
"GenomeBuild"
public static final String
"HG17"
public static final String
"HG18"
public static final String
"HG19"
public static final String
"IlmnID"
public static final String
"IlmnStrand"
public static final String
"Intensity_Only"
public static final String
"MapInfo"
public static final String
"Name"
public static final String
"35"
public static final String
"36"
public static final String
"37"
public static final String
"Ploidy"
public static final String
"RefStrand"
public static final String
"SNP"
public static final String
"Source"
public static final String
"SourceSeq"
public static final String
"SourceStrand"
public static final String
"SourceVersion"
public static final String
"Species"
public static final String
"TopGenomicSeq"
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picard.arrays.illumina.IlluminaManifestRecord
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picard.arrays.illumina.InfiniumDataFile
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picard.arrays.illumina.InfiniumEGTFile
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picard.arrays.illumina.InfiniumGTCFile
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picard.arrays.illumina.InfiniumVcfFieldsModifier and TypeConstant FieldValue
public static final String
"ALLELE_A"
public static final String
"ALLELE_B"
public static final String
"analysisVersionNumber"
public static final String
"arrayType"
public static final String
"autocallDate"
public static final String
"autocallGender"
public static final String
"autocallVersion"
public static final String
"BAF"
public static final String
"BEADSET_ID"
public static final String
"chipWellBarcode"
public static final String
"clusterFile"
public static final String
"DUPE"
public static final String
"expectedGender"
public static final String
"extendedManifestFile"
public static final String
"extendedIlluminaManifestVersion"
public static final String
"FAIL_REF"
public static final String
"fingerprintGender"
public static final String
"GC_SCORE"
public static final String
"GTA"
public static final String
"gtcCallRate"
public static final String
"gtcCallRateDetail"
public static final String
"GTZ"
public static final String
"IGC"
public static final String
"ILLUMINA_BUILD"
public static final String
"ILLUMINA_CHR"
public static final String
"ILLUMINA_POS"
public static final String
"ILLUMINA_STRAND"
public static final String
"imagingDate"
public static final String
"LRR"
public static final String
"manifestFile"
public static final String
"NORMX"
public static final String
"NORMY"
public static final String
"p95Green"
public static final String
"p95Red"
public static final String
"pipelineVersion"
public static final String
"PROBE_A"
public static final String
"PROBE_B"
public static final String
"R"
public static final String
"refSNP"
public static final String
"sampleAlias"
public static final String
"scannerName"
public static final String
"SOURCE"
public static final String
"THETA"
public static final String
"TRIALLELIC"
public static final String
"X"
public static final String
"Y"
public static final String
"zcallThresholds"
public static final String
"zcallVersion"
public static final String
"ZEROED_OUT_ASSAY"
public static final String
"zthresh_X"
public static final String
"zthresh_Y"
picard.cmdline.*
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picard.cmdline.StandardOptionDefinitionsModifier and TypeConstant FieldValue
public static final String
"ASO"
public static final String
"AS"
public static final String
"INSERT"
public static final String
"I"
public static final String
"L"
public static final String
"LIB"
public static final String
"M"
public static final String
"LOD"
public static final String
"MQ"
public static final String
"O"
public static final String
"PF"
public static final String
"PG"
public static final String
"RG"
public static final String
"R"
public static final String
"ALIAS"
public static final String
"SD"
public static final String
"SO"
public static final String
"OQ"
picard.fingerprint.*
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picard.fingerprint.CalculateFingerprintMetricsModifier and TypeConstant FieldValue
public final double
3.0
public final int
100
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picard.fingerprint.CheckFingerprint
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picard.fingerprint.FingerprintCheckerModifier and TypeConstant FieldValue
public static final double
0.01
public static final int
20
public static final int
10
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picard.fingerprint.HaplotypeMap
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picard.fingerprint.LiftOverHaplotypeMapModifier and TypeConstant FieldValue
public static final int
101
picard.illumina.*
-
picard.illumina.ExtractBarcodesProgram
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picard.illumina.IlluminaBasecallsToSam
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picard.illumina.parser.MultiTileBclParserModifier and TypeConstant FieldValue
public static final byte
MASKING_QUALITY
0x2
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picard.illumina.parser.ParameterizedFileUtilModifier and TypeConstant FieldValue
protected static final boolean
true
public static final String
"s_(\\d+)_(\\d{1,5})"
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picard.illumina.parser.ReadStructureModifier and TypeConstant FieldValue
public static final String
"A description of the logical structure of clusters in an Illumina Run, i.e. a description of the structure IlluminaBasecallsToSam assumes the data to be in. It should consist of integer/character pairs describing the number of cycles and the type of those cycles (B for Sample Barcode, M for molecular barcode, T for Template, and S for skip). E.g. If the input data consists of 80 base clusters and we provide a read structure of \"28T8M8B8S28T\" then the sequence may be split up into four reads:\n* read one with 28 cycles (bases) of template\n* read two with 8 cycles (bases) of molecular barcode (ex. unique molecular barcode)\n* read three with 8 cycles (bases) of sample barcode\n* 8 cycles (bases) skipped.\n* read four with 28 cycles (bases) of template\nThe skipped cycles would NOT be included in an output SAM/BAM file or in read groups therein."
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picard.illumina.parser.readers.AbstractIlluminaPositionFileReaderModifier and TypeConstant FieldValue
public static final float
1.0E7f
public static final float
-10.0f
public static final String
"s.locs"
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picard.illumina.parser.readers.BaseBclReader
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picard.illumina.parser.readers.BclQualityEvaluationStrategy
-
picard.illumina.parser.readers.FilterFileReader
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picard.illumina.quality.CollectHiSeqXPfFailMetrics
picard.metrics.*
-
picard.metrics.MultiLevelCollector<METRIC_TYPE extends htsjdk.samtools.metrics.MetricBase,
Histogram_KEY extends Comparable, ARGTYPE>
picard.sam.*
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picard.sam.AbstractAlignmentMerger
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picard.sam.AddOrReplaceReadGroups
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picard.sam.DownsampleSam
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picard.sam.SplitSamByLibrary
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picard.sam.markduplicates.MarkDuplicates
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picard.sam.markduplicates.MarkDuplicatesForFlowHelper
-
picard.sam.markduplicates.util.OpticalDuplicateFinderModifier and TypeConstant FieldValue
public static final int
1000
public static final int
300000
public static final int
100
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picard.sam.markduplicates.util.ReadEnds
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picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
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picard.sam.SamErrorMetric.ReadBaseStratification
-
picard.sam.util.PhysicalLocation
picard.util.*
-
picard.util.AdapterMarkerModifier and TypeConstant FieldValue
public static final int
30
public static final int
1
public static final int
100
-
picard.util.AsyncIterator<T>
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picard.util.ClippingUtilityModifier and TypeConstant FieldValue
public static final double
0.1
public static final double
0.1
public static final int
12
public static final int
6
public static final int
-1
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picard.util.IlluminaUtil
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picard.util.LiftoverUtils
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picard.util.MathUtilModifier and TypeConstant FieldValue
public static final double
0.9999999999999999
-
picard.util.help.HelpConstantsModifier and TypeConstant FieldValue
public static final String
"Base Calling"
public static final String
"Tools that process sequencing machine data, e.g. Illumina base calls, and detect sequencing level attributes, e.g. adapters"
public static final String
"Diagnostics and Quality Control"
public static final String
"Tools that collect sequencing quality related and comparative metrics"
public static final String
"Genotyping Arrays Manipulation"
public static final String
"Tools that manipulate data generated by Genotyping arrays"
public static final String
"Intervals Manipulation"
public static final String
"Tools that process genomic intervals in various formats"
public static final String
"Metrics"
public static final String
"Metrics"
public static final String
"Other"
public static final String
"Miscellaneous tools, e.g. those that aid in data streaming"
public static final String
"Read Data Manipulation"
public static final String
"Tools that manipulate read data in SAM, BAM or CRAM format"
public static final String
"Reference"
public static final String
"Tools that analyze and manipulate FASTA format references"
public static final String
"Test Tools"
public static final String
"Tools for internal test purposes"
public static final String
"Variant Evaluation and Refinement"
public static final String
"Tools that evaluate and refine variant calls, e.g. with annotations not offered by the engine"
public static final String
"Variant Filtering"
public static final String
"Tools that filter variants by annotating the FILTER column"
public static final String
"Variant Manipulation"
public static final String
"Tools that manipulate variant call format (VCF) data"
public static final String
"exclude"
public static final String
"tools"
public static final String
"utilities"
picard.vcf.*
-
picard.vcf.GenotypeConcordanceModifier and TypeConstant FieldValue
public static final String
".genotype_concordance_contingency_metrics"
public static final String
"CONC_ST"
public static final String
".genotype_concordance_detail_metrics"
public static final String
"call"
public static final String
".genotype_concordance.vcf.gz"
public static final String
"truth"
public static final String
".genotype_concordance_summary_metrics"
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picard.vcf.LiftoverVcfModifier and TypeConstant FieldValue
public static final String
"AttemptedAlleles"
public static final String
"AttemptedLocus"
public static final String
"CannotLiftOver"
public static final String
"IndelStraddlesMultipleIntevals"
public static final String
"MismatchedRefAllele"
public static final String
"NoTarget"
public static final String
"OriginalAlleles"
public static final String
"OriginalContig"
public static final String
"OriginalStart"
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picard.vcf.VcfToIntervalList
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picard.vcf.filter.AlleleBalanceFilter
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picard.vcf.filter.FilterApplyingVariantIterator
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picard.vcf.filter.QdFilter