Uses of Class
picard.cmdline.Option

Packages that use Option

Package	Description
picard.analysis
picard.analysis.artifacts
picard.analysis.directed
picard.analysis.replicates
picard.cmdline
picard.fastq
picard.fingerprint
picard.illumina
picard.illumina.quality
picard.reference
picard.sam
picard.sam.markduplicates
picard.sam.markduplicates.util
picard.util
picard.vcf
picard.vcf.filter

Uses of Option in picard.analysis

Fields in picard.analysis with annotations of type Option

Modifier and Type	Field and Description
java.util.List<java.lang.String>	CollectAlignmentSummaryMetrics.ADAPTER_SEQUENCE
boolean	CollectBaseDistributionByCycle.ALIGNED_READS_ONLY
boolean	MeanQualityByCycle.ALIGNED_READS_ONLY
boolean	QualityScoreDistribution.ALIGNED_READS_ONLY
boolean	CollectMultipleMetrics.ASSUME_SORTED
boolean	CollectRrbsMetrics.ASSUME_SORTED
boolean	SinglePassSamProgram.ASSUME_SORTED
int	CollectRrbsMetrics.C_QUALITY_THRESHOLD
java.io.File	CollectBaseDistributionByCycle.CHART_OUTPUT
java.io.File	CollectGcBiasMetrics.CHART_OUTPUT
java.io.File	CollectRnaSeqMetrics.CHART_OUTPUT
java.io.File	CollectWgsMetricsWithNonZeroCoverage.CHART_OUTPUT
java.io.File	MeanQualityByCycle.CHART_OUTPUT
java.io.File	QualityScoreDistribution.CHART_OUTPUT
int	CollectJumpingLibraryMetrics.CHIMERA_KB_MIN
int	CollectOxoGMetrics.CONTEXT_SIZE
java.util.Set<java.lang.String>	CollectOxoGMetrics.CONTEXTS
boolean	CollectWgsMetrics.COUNT_UNPAIRED
int	CollectRawWgsMetrics.COVERAGE_CAP
int	CollectWgsMetrics.COVERAGE_CAP
java.io.File	CollectMultipleMetrics.DB_SNP
java.io.File	CollectOxoGMetrics.DB_SNP
double	CollectInsertSizeMetrics.DEVIATIONS
java.util.Set<htsjdk.samtools.SamPairUtil.PairOrientation>	CollectAlignmentSummaryMetrics.EXPECTED_PAIR_ORIENTATIONS
java.lang.String	CollectMultipleMetrics.FILE_EXTENSION
java.lang.Long	CollectWgsMetricsFromQuerySorted.GENOME_TERRITORY Deprecated.
java.io.File	CollectInsertSizeMetrics.Histogram_FILE
java.lang.Integer	CollectInsertSizeMetrics.HISTOGRAM_WIDTH
java.util.Set<java.lang.String>	CollectRnaSeqMetrics.IGNORE_SEQUENCE
boolean	CollectWgsMetrics.INCLUDE_BQ_HISTOGRAM
boolean	CollectInsertSizeMetrics.INCLUDE_DUPLICATES
boolean	QualityScoreDistribution.INCLUDE_NO_CALLS
boolean	CollectQualityYieldMetrics.INCLUDE_SECONDARY_ALIGNMENTS
boolean	CollectQualityYieldMetrics.INCLUDE_SUPPLEMENTAL_ALIGNMENTS
java.util.List<java.io.File>	CollectJumpingLibraryMetrics.INPUT
java.io.File	CollectMultipleMetrics.INPUT
java.io.File	CollectOxoGMetrics.INPUT
java.io.File	CollectRrbsMetrics.INPUT
java.io.File	CollectWgsMetrics.INPUT
java.io.File	CollectWgsMetricsFromQuerySorted.INPUT Deprecated.
java.io.File	SinglePassSamProgram.INPUT
java.io.File	CollectMultipleMetrics.INTERVALS
java.io.File	CollectOxoGMetrics.INTERVALS
java.io.File	CollectWgsMetrics.INTERVALS
java.io.File	CollectWgsMetricsFromSampledSites.INTERVALS Deprecated.
boolean	CollectAlignmentSummaryMetrics.IS_BISULFITE_SEQUENCED
boolean	CollectGcBiasMetrics.IS_BISULFITE_SEQUENCED
int	CollectRawWgsMetrics.LOCUS_ACCUMULATION_CAP
int	CollectWgsMetrics.LOCUS_ACCUMULATION_CAP
int	CollectAlignmentSummaryMetrics.MAX_INSERT_SIZE
double	CollectRrbsMetrics.MAX_MISMATCH_RATE
int	CollectOxoGMetrics.MAXIMUM_INSERT_SIZE
java.util.Set<MetricAccumulationLevel>	CollectAlignmentSummaryMetrics.METRIC_ACCUMULATION_LEVEL
java.util.Set<MetricAccumulationLevel>	CollectGcBiasMetrics.METRIC_ACCUMULATION_LEVEL
java.util.Set<MetricAccumulationLevel>	CollectInsertSizeMetrics.METRIC_ACCUMULATION_LEVEL
java.util.Set<MetricAccumulationLevel>	CollectMultipleMetrics.METRIC_ACCUMULATION_LEVEL
java.util.Set<MetricAccumulationLevel>	CollectRnaSeqMetrics.METRIC_ACCUMULATION_LEVEL
java.util.Set<MetricAccumulationLevel>	CollectRrbsMetrics.METRIC_ACCUMULATION_LEVEL
java.lang.String	CollectRrbsMetrics.METRICS_FILE_PREFIX
int	CollectRawWgsMetrics.MINIMUM_BASE_QUALITY
int	CollectWgsMetrics.MINIMUM_BASE_QUALITY
double	CollectGcBiasMetrics.MINIMUM_GENOME_FRACTION
int	CollectOxoGMetrics.MINIMUM_INSERT_SIZE
int	CollectRnaSeqMetrics.MINIMUM_LENGTH
java.lang.Integer	CollectJumpingLibraryMetrics.MINIMUM_MAPPING_QUALITY
int	CollectOxoGMetrics.MINIMUM_MAPPING_QUALITY
int	CollectRawWgsMetrics.MINIMUM_MAPPING_QUALITY
int	CollectWgsMetrics.MINIMUM_MAPPING_QUALITY
float	CollectInsertSizeMetrics.MINIMUM_PCT
int	CollectOxoGMetrics.MINIMUM_QUALITY_SCORE
int	CollectWgsMetricsFromQuerySorted.MINIMUM_RAW_BASE_QUALITY Deprecated.
int	CollectWgsMetricsFromQuerySorted.MINIMUM_RAW_MAPPING_QUALITY Deprecated.
int	CollectRrbsMetrics.MINIMUM_READ_LENGTH
int	CollectWgsMetricsFromQuerySorted.MINIMUM_USABLE_BASE_QUALITY Deprecated.
int	CollectWgsMetricsFromQuerySorted.MINIMUM_USABLE_MAPPING_QUALITY Deprecated.
int	CollectRrbsMetrics.NEXT_BASE_QUALITY_THRESHOLD
java.io.File	CollectJumpingLibraryMetrics.OUTPUT
java.lang.String	CollectMultipleMetrics.OUTPUT
java.io.File	CollectOxoGMetrics.OUTPUT
java.io.File	CollectWgsMetrics.OUTPUT
java.io.File	CollectWgsMetricsFromQuerySorted.OUTPUT Deprecated.
java.io.File	SinglePassSamProgram.OUTPUT
boolean	CollectBaseDistributionByCycle.PF_READS_ONLY
boolean	MeanQualityByCycle.PF_READS_ONLY
boolean	QualityScoreDistribution.PF_READS_ONLY
java.util.Set<CollectMultipleMetrics.Program>	CollectMultipleMetrics.PROGRAM
java.io.File	CollectRnaSeqMetrics.REF_FLAT
java.io.File	CollectRrbsMetrics.REFERENCE
java.io.File	CollectAlignmentSummaryMetrics.REFERENCE_SEQUENCE
java.io.File	CollectOxoGMetrics.REFERENCE_SEQUENCE
java.io.File	CollectWgsMetrics.REFERENCE_SEQUENCE
java.io.File	CollectRnaSeqMetrics.RIBOSOMAL_INTERVALS
double	CollectRnaSeqMetrics.RRNA_FRAGMENT_PERCENTAGE
int	CollectWgsMetrics.SAMPLE_SIZE
int	CollectGcBiasMetrics.SCAN_WINDOW_SIZE
java.util.Set<java.lang.String>	CollectRrbsMetrics.SEQUENCE_NAMES
int	CollectMultipleMetrics.STOP_AFTER
int	CollectOxoGMetrics.STOP_AFTER
long	CollectWgsMetrics.STOP_AFTER
long	SinglePassSamProgram.STOP_AFTER
RnaSeqMetricsCollector.StrandSpecificity	CollectRnaSeqMetrics.STRAND_SPECIFICITY
java.io.File	CollectGcBiasMetrics.SUMMARY_OUTPUT
int	CollectJumpingLibraryMetrics.TAIL_LIMIT
boolean	CollectOxoGMetrics.USE_OQ
boolean	CollectQualityYieldMetrics.USE_ORIGINAL_QUALITIES

Uses of Option in picard.analysis.artifacts

Fields in picard.analysis.artifacts with annotations of type Option

Modifier and Type	Field and Description
int	CollectSequencingArtifactMetrics.CONTEXT_SIZE
java.util.Set<java.lang.String>	CollectSequencingArtifactMetrics.CONTEXTS_TO_PRINT
java.io.File	CollectSequencingArtifactMetrics.DB_SNP
java.lang.String	CollectSequencingArtifactMetrics.FILE_EXTENSION
boolean	CollectSequencingArtifactMetrics.INCLUDE_UNPAIRED
java.io.File	ConvertSequencingArtifactToOxoG.INPUT_BASE
java.io.File	CollectSequencingArtifactMetrics.INTERVALS
int	CollectSequencingArtifactMetrics.MAXIMUM_INSERT_SIZE
int	CollectSequencingArtifactMetrics.MINIMUM_INSERT_SIZE
int	CollectSequencingArtifactMetrics.MINIMUM_MAPPING_QUALITY
int	CollectSequencingArtifactMetrics.MINIMUM_QUALITY_SCORE
java.io.File	ConvertSequencingArtifactToOxoG.OUTPUT_BASE
boolean	CollectSequencingArtifactMetrics.TANDEM_READS
boolean	CollectSequencingArtifactMetrics.USE_OQ

Uses of Option in picard.analysis.directed

Fields in picard.analysis.directed with annotations of type Option

Modifier and Type	Field and Description
java.io.File	CollectTargetedPcrMetrics.AMPLICON_INTERVALS
java.util.List<java.io.File>	CollectHsMetrics.BAIT_INTERVALS
java.lang.String	CollectHsMetrics.BAIT_SET_NAME
boolean	CalculateHsMetrics.CLIP_OVERLAPPING_READS Deprecated.
boolean	CollectHsMetrics.CLIP_OVERLAPPING_READS
boolean	CollectTargetedMetrics.CLIP_OVERLAPPING_READS
int	CollectTargetedMetrics.COVERAGE_CAP
java.lang.String	CollectTargetedPcrMetrics.CUSTOM_AMPLICON_SET_NAME
java.io.File	CollectTargetedMetrics.INPUT
java.util.Set<MetricAccumulationLevel>	CollectTargetedMetrics.METRIC_ACCUMULATION_LEVEL
int	CalculateHsMetrics.MINIMUM_BASE_QUALITY Deprecated.
int	CollectHsMetrics.MINIMUM_BASE_QUALITY
int	CollectTargetedMetrics.MINIMUM_BASE_QUALITY
int	CalculateHsMetrics.MINIMUM_MAPPING_QUALITY Deprecated.
int	CollectHsMetrics.MINIMUM_MAPPING_QUALITY
int	CollectTargetedMetrics.MINIMUM_MAPPING_QUALITY
int	CollectTargetedMetrics.NEAR_DISTANCE
java.io.File	CollectTargetedMetrics.OUTPUT
java.io.File	CollectTargetedMetrics.PER_BASE_COVERAGE
java.io.File	CollectTargetedMetrics.PER_TARGET_COVERAGE
int	CollectTargetedMetrics.SAMPLE_SIZE
java.util.List<java.io.File>	CollectTargetedMetrics.TARGET_INTERVALS

Uses of Option in picard.analysis.replicates

Fields in picard.analysis.replicates with annotations of type Option

Modifier and Type	Field and Description
java.lang.String	CollectIndependentReplicateMetrics.BARCODE_BQ
java.lang.String	CollectIndependentReplicateMetrics.BARCODE_TAG
java.io.File	CollectIndependentReplicateMetrics.INPUT
java.io.File	CollectIndependentReplicateMetrics.MATRIX_OUTPUT
java.lang.Integer	CollectIndependentReplicateMetrics.MINIMUM_BARCODE_BQ
java.lang.Integer	CollectIndependentReplicateMetrics.MINIMUM_BQ
java.lang.Integer	CollectIndependentReplicateMetrics.MINIMUM_GQ
java.lang.Integer	CollectIndependentReplicateMetrics.MINIMUM_MQ
java.io.File	CollectIndependentReplicateMetrics.OUTPUT
java.lang.String	CollectIndependentReplicateMetrics.SAMPLE
java.lang.Integer	CollectIndependentReplicateMetrics.STOP_AFTER
java.io.File	CollectIndependentReplicateMetrics.VCF

Uses of Option in picard.cmdline

Fields in picard.cmdline with annotations of type Option

Modifier and Type	Field and Description
int	CommandLineProgram.COMPRESSION_LEVEL
java.lang.Boolean	CommandLineProgram.CREATE_INDEX
boolean	CommandLineProgram.CREATE_MD5_FILE
java.lang.String	CommandLineProgram.GA4GH_CLIENT_SECRETS
java.lang.Integer	CommandLineProgram.MAX_RECORDS_IN_RAM
java.lang.Boolean	CommandLineProgram.QUIET
java.io.File	CommandLineProgram.REFERENCE_SEQUENCE
java.util.List<java.io.File>	CommandLineProgram.TMP_DIR
htsjdk.samtools.ValidationStringency	CommandLineProgram.VALIDATION_STRINGENCY
htsjdk.samtools.util.Log.LogLevel	CommandLineProgram.VERBOSITY

Uses of Option in picard.fastq

Fields in picard.fastq with annotations of type Option

Modifier and Type	Field and Description
java.io.File	BamToBfq.ANALYSIS_DIR
java.lang.Integer	BamToBfq.BASES_TO_WRITE
boolean	BamToBfq.CLIP_ADAPTERS
java.lang.String	BamToBfq.FLOWCELL_BARCODE
java.lang.Boolean	BamToBfq.INCLUDE_NON_PF_READS
java.io.File	BamToBfq.INPUT
java.lang.Integer	BamToBfq.LANE
java.lang.String	BamToBfq.OUTPUT_FILE_PREFIX
java.lang.Boolean	BamToBfq.PAIRED_RUN
java.lang.Integer	BamToBfq.READ_CHUNK_SIZE
java.lang.String	BamToBfq.READ_NAME_PREFIX
java.lang.Integer	BamToBfq.READS_TO_ALIGN
java.lang.String	BamToBfq.RUN_BARCODE

Uses of Option in picard.fingerprint

Fields in picard.fingerprint with annotations of type Option

Modifier and Type	Field and Description
boolean	CrosscheckReadGroupFingerprints.ALLOW_DUPLICATE_READS
boolean	CrosscheckReadGroupFingerprints.CROSSCHECK_LIBRARIES
boolean	CrosscheckReadGroupFingerprints.CROSSCHECK_SAMPLES
java.io.File	CheckFingerprint.DETAIL_OUTPUT
int	CrosscheckReadGroupFingerprints.EXIT_CODE_WHEN_MISMATCH
boolean	CrosscheckReadGroupFingerprints.EXPECT_ALL_READ_GROUPS_TO_MATCH
double	CheckFingerprint.GENOTYPE_LOD_THRESHOLD
java.io.File	CheckFingerprint.GENOTYPES
double	CrosscheckReadGroupFingerprints.GENOTYPING_ERROR_RATE
java.io.File	CheckFingerprint.HAPLOTYPE_MAP
java.io.File	CrosscheckReadGroupFingerprints.HAPLOTYPE_MAP
boolean	CheckFingerprint.IGNORE_READ_GROUPS
java.io.File	CheckFingerprint.INPUT
java.util.List<java.io.File>	CrosscheckReadGroupFingerprints.INPUT
double	CrosscheckReadGroupFingerprints.LOD_THRESHOLD
double	CrosscheckReadGroupFingerprints.LOSS_OF_HET_RATE
int	CrosscheckReadGroupFingerprints.NUM_THREADS
java.lang.String	CheckFingerprint.OUTPUT
java.io.File	CrosscheckReadGroupFingerprints.OUTPUT
boolean	CrosscheckReadGroupFingerprints.OUTPUT_ERRORS_ONLY
java.lang.String	CheckFingerprint.SAMPLE_ALIAS
java.io.File	CheckFingerprint.SUMMARY_OUTPUT

Uses of Option in picard.illumina

Fields in picard.illumina with annotations of type Option

Modifier and Type	Field and Description
int	MarkIlluminaAdapters.ADAPTER_TRUNCATION_LENGTH
java.util.List<IlluminaUtil.IlluminaAdapterPair>	MarkIlluminaAdapters.ADAPTERS
java.util.List<IlluminaUtil.IlluminaAdapterPair>	IlluminaBasecallsToFastq.ADAPTERS_TO_CHECK
java.util.List<IlluminaUtil.IlluminaAdapterPair>	IlluminaBasecallsToSam.ADAPTERS_TO_CHECK
boolean	IlluminaBasecallsToFastq.APPLY_EAMSS_FILTER
boolean	IlluminaBasecallsToSam.APPLY_EAMSS_FILTER
java.util.List<java.lang.String>	ExtractIlluminaBarcodes.BARCODE
java.io.File	ExtractIlluminaBarcodes.BARCODE_FILE
java.io.File	IlluminaBasecallsToSam.BARCODE_PARAMS
java.io.File	IlluminaBasecallsToFastq.BARCODES_DIR
java.io.File	IlluminaBasecallsToSam.BARCODES_DIR
java.io.File	CheckIlluminaDirectory.BASECALLS_DIR
java.io.File	CollectIlluminaBasecallingMetrics.BASECALLS_DIR
java.io.File	ExtractIlluminaBarcodes.BASECALLS_DIR
java.io.File	IlluminaBasecallsToFastq.BASECALLS_DIR
java.io.File	IlluminaBasecallsToSam.BASECALLS_DIR
boolean	ExtractIlluminaBarcodes.COMPRESS_OUTPUTS
boolean	IlluminaBasecallsToFastq.COMPRESS_OUTPUTS
java.util.Set<IlluminaDataType>	CheckIlluminaDirectory.DATA_TYPES
java.lang.Boolean	CheckIlluminaDirectory.FAKE_FILES
java.lang.Integer	IlluminaBasecallsToFastq.FIRST_TILE
java.lang.Integer	IlluminaBasecallsToSam.FIRST_TILE
java.lang.String	MarkIlluminaAdapters.FIVE_PRIME_ADAPTER
java.lang.String	IlluminaBasecallsToFastq.FLOWCELL_BARCODE
java.lang.Boolean	IlluminaBasecallsToFastq.FORCE_GC
java.lang.Boolean	IlluminaBasecallsToSam.FORCE_GC
boolean	IlluminaBasecallsToFastq.IGNORE_UNEXPECTED_BARCODES
boolean	IlluminaBasecallsToSam.IGNORE_UNEXPECTED_BARCODES
boolean	IlluminaBasecallsToFastq.INCLUDE_NON_PF_READS
boolean	IlluminaBasecallsToSam.INCLUDE_NON_PF_READS
java.io.File	CollectIlluminaBasecallingMetrics.INPUT
java.io.File	MarkIlluminaAdapters.INPUT
java.lang.Integer	CollectIlluminaBasecallingMetrics.LANE
java.lang.Integer	ExtractIlluminaBarcodes.LANE
java.lang.Integer	IlluminaBasecallsToFastq.LANE
java.lang.Integer	IlluminaBasecallsToSam.LANE
java.util.List<java.lang.Integer>	CheckIlluminaDirectory.LANES
java.lang.String	IlluminaBasecallsToSam.LIBRARY_NAME
java.io.File	IlluminaBasecallsToSam.LIBRARY_PARAMS
java.lang.Boolean	CheckIlluminaDirectory.LINK_LOCS
java.lang.String	IlluminaBasecallsToFastq.MACHINE_NAME
double	MarkIlluminaAdapters.MAX_ERROR_RATE_PE
double	MarkIlluminaAdapters.MAX_ERROR_RATE_SE
int	ExtractIlluminaBarcodes.MAX_MISMATCHES
int	ExtractIlluminaBarcodes.MAX_NO_CALLS
int	IlluminaBasecallsToFastq.MAX_READS_IN_RAM_PER_TILE
int	IlluminaBasecallsToSam.MAX_READS_IN_RAM_PER_TILE
java.io.File	MarkIlluminaAdapters.METRICS
java.io.File	ExtractIlluminaBarcodes.METRICS_FILE
int	MarkIlluminaAdapters.MIN_MATCH_BASES_PE
int	MarkIlluminaAdapters.MIN_MATCH_BASES_SE
int	ExtractIlluminaBarcodes.MIN_MISMATCH_DELTA
int	ExtractIlluminaBarcodes.MINIMUM_BASE_QUALITY
int	ExtractIlluminaBarcodes.MINIMUM_QUALITY
int	IlluminaBasecallsToFastq.MINIMUM_QUALITY
int	IlluminaBasecallsToSam.MINIMUM_QUALITY
java.lang.String	IlluminaBasecallsToSam.MOLECULAR_INDEX_BASE_QUALITY_TAG
java.lang.String	IlluminaBasecallsToSam.MOLECULAR_INDEX_TAG
java.io.File	IlluminaBasecallsToFastq.MULTIPLEX_PARAMS
int	MarkIlluminaAdapters.NUM_ADAPTERS_TO_KEEP
int	ExtractIlluminaBarcodes.NUM_PROCESSORS
java.lang.Integer	IlluminaBasecallsToFastq.NUM_PROCESSORS
java.lang.Integer	IlluminaBasecallsToSam.NUM_PROCESSORS
java.io.File	CollectIlluminaBasecallingMetrics.OUTPUT
java.io.File	IlluminaBasecallsToSam.OUTPUT
java.io.File	MarkIlluminaAdapters.OUTPUT
java.io.File	ExtractIlluminaBarcodes.OUTPUT_DIR
java.io.File	CollectIlluminaLaneMetrics.OUTPUT_DIRECTORY
java.lang.String	CollectIlluminaLaneMetrics.OUTPUT_PREFIX
java.io.File	IlluminaBasecallsToFastq.OUTPUT_PREFIX
java.lang.Boolean	MarkIlluminaAdapters.PAIRED_RUN
java.lang.String	IlluminaBasecallsToSam.PLATFORM
int	MarkIlluminaAdapters.PRUNE_ADAPTER_LIST_AFTER_THIS_MANY_ADAPTERS_SEEN
java.lang.String	IlluminaBasecallsToSam.READ_GROUP_ID
IlluminaBasecallsToFastq.ReadNameFormat	IlluminaBasecallsToFastq.READ_NAME_FORMAT
java.lang.String	CheckIlluminaDirectory.READ_STRUCTURE
java.lang.String	CollectIlluminaBasecallingMetrics.READ_STRUCTURE
ReadStructure	CollectIlluminaLaneMetrics.READ_STRUCTURE
java.lang.String	ExtractIlluminaBarcodes.READ_STRUCTURE
java.lang.String	IlluminaBasecallsToFastq.READ_STRUCTURE
java.lang.String	IlluminaBasecallsToSam.READ_STRUCTURE
java.lang.String	IlluminaBasecallsToFastq.RUN_BARCODE
java.lang.String	IlluminaBasecallsToSam.RUN_BARCODE
java.io.File	CollectIlluminaLaneMetrics.RUN_DIRECTORY
java.util.Date	IlluminaBasecallsToSam.RUN_START_DATE
java.lang.String	IlluminaBasecallsToSam.SAMPLE_ALIAS
java.lang.String	IlluminaBasecallsToSam.SEQUENCING_CENTER
java.util.List<java.lang.String>	IlluminaBasecallsToSam.TAG_PER_MOLECULAR_INDEX
java.lang.String	MarkIlluminaAdapters.THREE_PRIME_ADAPTER
java.lang.Integer	IlluminaBasecallsToFastq.TILE_LIMIT
java.lang.Integer	IlluminaBasecallsToSam.TILE_LIMIT
java.util.List<java.lang.Integer>	CheckIlluminaDirectory.TILE_NUMBERS

Uses of Option in picard.illumina.quality

Fields in picard.illumina.quality with annotations of type Option

Modifier and Type	Field and Description
java.io.File	CollectHiSeqXPfFailMetrics.BASECALLS_DIR
java.lang.Integer	CollectHiSeqXPfFailMetrics.LANE
int	CollectHiSeqXPfFailMetrics.N_CYCLES
int	CollectHiSeqXPfFailMetrics.NUM_PROCESSORS
java.io.File	CollectHiSeqXPfFailMetrics.OUTPUT
double	CollectHiSeqXPfFailMetrics.PROB_EXPLICIT_READS

Uses of Option in picard.reference

Fields in picard.reference with annotations of type Option

Modifier and Type	Field and Description
java.io.File	NonNFastaSize.INPUT
java.io.File	NormalizeFasta.INPUT
java.io.File	ExtractSequences.INTERVAL_LIST
java.io.File	NonNFastaSize.INTERVALS
int	ExtractSequences.LINE_LENGTH
int	NormalizeFasta.LINE_LENGTH
java.io.File	ExtractSequences.OUTPUT
java.io.File	NonNFastaSize.OUTPUT
java.io.File	NormalizeFasta.OUTPUT
java.io.File	ExtractSequences.REFERENCE_SEQUENCE
boolean	NormalizeFasta.TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE

Uses of Option in picard.sam

Fields in picard.sam with annotations of type Option

Modifier and Type	Field and Description
double	DownsampleSam.ACCURACY
java.lang.Boolean	FixMateInformation.ADD_MATE_CIGAR
java.lang.Boolean	MergeBamAlignment.ADD_MATE_CIGAR
java.util.List<java.io.File>	MergeBamAlignment.ALIGNED_BAM
boolean	MergeBamAlignment.ALIGNED_READS_ONLY
boolean	MergeBamAlignment.ALIGNER_PROPER_PAIR_FLAGS
ViewSam.AlignmentStatus	ViewSam.ALIGNMENT_STATUS
java.lang.Boolean	FastqToSam.ALLOW_AND_IGNORE_EMPTY_LINES
boolean	ReorderSam.ALLOW_CONTIG_LENGTH_DISCORDANCE
boolean	ReorderSam.ALLOW_INCOMPLETE_DICT_CONCORDANCE
boolean	PositionBasedDownsampleSam.ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS
boolean	FixMateInformation.ASSUME_SORTED
boolean	MergeSamFiles.ASSUME_SORTED
java.util.List<java.lang.String>	RevertSam.ATTRIBUTE_TO_CLEAR
java.util.List<java.lang.String>	MergeBamAlignment.ATTRIBUTES_TO_REMOVE
java.util.List<java.lang.String>	MergeBamAlignment.ATTRIBUTES_TO_RETAIN
boolean	MergeBamAlignment.CLIP_ADAPTERS
boolean	MergeBamAlignment.CLIP_OVERLAPPING_READS
java.lang.String	SamToFastq.CLIPPING_ACTION
java.lang.String	SamToFastq.CLIPPING_ATTRIBUTE
int	SamToFastq.CLIPPING_MIN_LENGTH
java.util.List<java.lang.String>	AddCommentsToBam.COMMENT
java.util.List<java.lang.String>	FastqToSam.COMMENT
java.util.List<java.lang.String>	MergeSamFiles.COMMENT
java.lang.String	FastqToSam.DESCRIPTION
java.util.List<htsjdk.samtools.SamPairUtil.PairOrientation>	MergeBamAlignment.EXPECTED_ORIENTATIONS
java.io.File	FastqToSam.FASTQ
java.io.File	SamToFastq.FASTQ
java.io.File	FastqToSam.FASTQ2
FilterSamReads.Filter	FilterSamReads.FILTER
java.lang.Double	PositionBasedDownsampleSam.FRACTION
java.lang.String	CreateSequenceDictionary.GENOME_ASSEMBLY
java.io.File	ReplaceSamHeader.HEADER
boolean	ViewSam.HEADER_ONLY
java.util.List<htsjdk.samtools.SAMValidationError.Type>	ValidateSamFile.IGNORE
java.lang.Boolean	FixMateInformation.IGNORE_MISSING_MATES
boolean	ValidateSamFile.IGNORE_WARNINGS
boolean	SamToFastq.INCLUDE_NON_PF_READS
boolean	SamToFastq.INCLUDE_NON_PRIMARY_ALIGNMENTS
boolean	MergeBamAlignment.INCLUDE_SECONDARY_ALIGNMENTS
htsjdk.samtools.BamIndexValidator.IndexValidationStringency	ValidateSamFile.INDEX_VALIDATION_STRINGENCY
java.io.File	AddCommentsToBam.INPUT
java.lang.String	AddOrReplaceReadGroups.INPUT
java.io.File	BamIndexStats.INPUT
java.lang.String	BuildBamIndex.INPUT
java.io.File	CalculateReadGroupChecksum.INPUT
java.io.File	CheckTerminatorBlock.INPUT
java.io.File	CleanSam.INPUT
java.io.File	DownsampleSam.INPUT
java.io.File	FilterSamReads.INPUT
java.util.List<java.io.File>	FixMateInformation.INPUT
java.util.List<java.io.File>	GatherBamFiles.INPUT
java.util.List<java.io.File>	MergeSamFiles.INPUT
java.io.File	PositionBasedDownsampleSam.INPUT
java.io.File	ReorderSam.INPUT
java.io.File	ReplaceSamHeader.INPUT
java.io.File	RevertOriginalBaseQualitiesAndAddMateCigar.INPUT
java.io.File	RevertSam.INPUT
java.io.File	SamFormatConverter.INPUT
java.io.File	SamToFastq.INPUT
java.io.File	SetNmAndUqTags.INPUT
java.io.File	SortSam.INPUT
java.io.File	SplitSamByLibrary.INPUT
java.io.File	ValidateSamFile.INPUT
java.lang.String	ViewSam.INPUT
boolean	SamToFastq.INTERLEAVE
java.io.File	ViewSam.INTERVAL_LIST
java.io.File	MergeSamFiles.INTERVALS
boolean	MergeBamAlignment.IS_BISULFITE_SEQUENCE
boolean	SetNmAndUqTags.IS_BISULFITE_SEQUENCE
boolean	ValidateSamFile.IS_BISULFITE_SEQUENCED
java.io.File	FilterSamReads.JAVASCRIPT_FILE
java.lang.Integer	MergeBamAlignment.JUMP_SIZE
java.lang.String	FastqToSam.LIBRARY_NAME
java.lang.String	RevertSam.LIBRARY_NAME
double	RevertSam.MAX_DISCARD_FRACTION
int	MergeBamAlignment.MAX_INSERTIONS_OR_DELETIONS
int	ValidateSamFile.MAX_OPEN_TEMP_FILES
java.lang.Integer	ValidateSamFile.MAX_OUTPUT
int	FastqToSam.MAX_Q
int	RevertOriginalBaseQualitiesAndAddMateCigar.MAX_RECORDS_TO_EXAMINE
boolean	MergeSamFiles.MERGE_SEQUENCE_DICTIONARIES
int	FastqToSam.MIN_Q
int	MergeBamAlignment.MIN_UNCLIPPED_BASES
ValidateSamFile.Mode	ValidateSamFile.MODE
int	CreateSequenceDictionary.NUM_SEQUENCES
java.io.File	AddCommentsToBam.OUTPUT
java.io.File	AddOrReplaceReadGroups.OUTPUT
java.io.File	BuildBamIndex.OUTPUT
java.io.File	CalculateReadGroupChecksum.OUTPUT
java.io.File	CleanSam.OUTPUT
java.io.File	CreateSequenceDictionary.OUTPUT
java.io.File	DownsampleSam.OUTPUT
java.io.File	FastqToSam.OUTPUT
java.io.File	FilterSamReads.OUTPUT
java.io.File	FixMateInformation.OUTPUT
java.io.File	GatherBamFiles.OUTPUT
java.io.File	MergeBamAlignment.OUTPUT
java.io.File	MergeSamFiles.OUTPUT
java.io.File	PositionBasedDownsampleSam.OUTPUT
java.io.File	ReorderSam.OUTPUT
java.io.File	ReplaceSamHeader.OUTPUT
java.io.File	RevertOriginalBaseQualitiesAndAddMateCigar.OUTPUT
java.io.File	RevertSam.OUTPUT
java.io.File	SamFormatConverter.OUTPUT
java.io.File	SetNmAndUqTags.OUTPUT
java.io.File	SortSam.OUTPUT
java.io.File	SplitSamByLibrary.OUTPUT
java.io.File	ValidateSamFile.OUTPUT
boolean	RevertSam.OUTPUT_BY_READGROUP
java.io.File	SamToFastq.OUTPUT_DIR
java.io.File	RevertSam.OUTPUT_MAP
boolean	SamToFastq.OUTPUT_PER_RG
java.lang.Boolean	MergeBamAlignment.PAIRED_RUN Deprecated.
ViewSam.PfStatus	ViewSam.PF_STATUS
java.lang.String	FastqToSam.PLATFORM
java.lang.String	FastqToSam.PLATFORM_MODEL
java.lang.String	FastqToSam.PLATFORM_UNIT
java.lang.Integer	FastqToSam.PREDICTED_INSERT_SIZE
picard.sam.MergeBamAlignment.PrimaryAlignmentStrategy	MergeBamAlignment.PRIMARY_ALIGNMENT_STRATEGY
double	DownsampleSam.PROBABILITY
java.lang.String	FastqToSam.PROGRAM_GROUP
java.lang.String	MergeBamAlignment.PROGRAM_GROUP_COMMAND_LINE
java.lang.String	MergeBamAlignment.PROGRAM_GROUP_NAME
java.lang.String	MergeBamAlignment.PROGRAM_GROUP_VERSION
java.lang.String	MergeBamAlignment.PROGRAM_RECORD_ID
java.lang.Integer	SamToFastq.QUALITY
htsjdk.samtools.util.FastqQualityFormat	FastqToSam.QUALITY_FORMAT
java.lang.Integer	DownsampleSam.RANDOM_SEED
boolean	SamToFastq.RE_REVERSE
java.lang.String	FastqToSam.READ_GROUP_NAME
java.io.File	FilterSamReads.READ_LIST_FILE
java.util.List<java.io.File>	MergeBamAlignment.READ1_ALIGNED_BAM
java.lang.Integer	SamToFastq.READ1_MAX_BASES_TO_WRITE
int	MergeBamAlignment.READ1_TRIM
int	SamToFastq.READ1_TRIM
java.util.List<java.io.File>	MergeBamAlignment.READ2_ALIGNED_BAM
java.lang.Integer	SamToFastq.READ2_MAX_BASES_TO_WRITE
int	MergeBamAlignment.READ2_TRIM
int	SamToFastq.READ2_TRIM
boolean	ViewSam.RECORDS_ONLY
java.io.File	CreateSequenceDictionary.REFERENCE
java.io.File	ReorderSam.REFERENCE
java.io.File	MergeBamAlignment.REFERENCE_SEQUENCE
boolean	RevertSam.REMOVE_ALIGNMENT_INFORMATION
boolean	PositionBasedDownsampleSam.REMOVE_DUPLICATE_INFORMATION
boolean	RevertSam.REMOVE_DUPLICATE_INFORMATION
boolean	RevertOriginalBaseQualitiesAndAddMateCigar.RESTORE_ORIGINAL_QUALITIES
boolean	RevertSam.RESTORE_ORIGINAL_QUALITIES
java.lang.String	SamToFastq.RG_TAG
java.lang.String	AddOrReplaceReadGroups.RGCN
java.lang.String	AddOrReplaceReadGroups.RGDS
htsjdk.samtools.util.Iso8601Date	AddOrReplaceReadGroups.RGDT
java.lang.String	AddOrReplaceReadGroups.RGID
java.lang.String	AddOrReplaceReadGroups.RGLB
java.lang.String	AddOrReplaceReadGroups.RGPG
java.lang.Integer	AddOrReplaceReadGroups.RGPI
java.lang.String	AddOrReplaceReadGroups.RGPL
java.lang.String	AddOrReplaceReadGroups.RGPM
java.lang.String	AddOrReplaceReadGroups.RGPU
java.lang.String	AddOrReplaceReadGroups.RGSM
htsjdk.samtools.util.Iso8601Date	FastqToSam.RUN_DATE
java.lang.String	RevertSam.SAMPLE_ALIAS
java.lang.String	FastqToSam.SAMPLE_NAME
boolean	RevertSam.SANITIZE
java.io.File	SamToFastq.SECOND_END_FASTQ
java.lang.String	FastqToSam.SEQUENCING_CENTER
htsjdk.samtools.SAMFileHeader.SortOrder	AddOrReplaceReadGroups.SORT_ORDER
htsjdk.samtools.SAMFileHeader.SortOrder	FastqToSam.SORT_ORDER
htsjdk.samtools.SAMFileHeader.SortOrder	FilterSamReads.SORT_ORDER
htsjdk.samtools.SAMFileHeader.SortOrder	FixMateInformation.SORT_ORDER
htsjdk.samtools.SAMFileHeader.SortOrder	MergeBamAlignment.SORT_ORDER
htsjdk.samtools.SAMFileHeader.SortOrder	MergeSamFiles.SORT_ORDER
htsjdk.samtools.SAMFileHeader.SortOrder	RevertOriginalBaseQualitiesAndAddMateCigar.SORT_ORDER
htsjdk.samtools.SAMFileHeader.SortOrder	RevertSam.SORT_ORDER
htsjdk.samtools.SAMFileHeader.SortOrder	SortSam.SORT_ORDER
java.lang.String	CreateSequenceDictionary.SPECIES
java.lang.Long	PositionBasedDownsampleSam.STOP_AFTER
htsjdk.samtools.DownsamplingIteratorFactory.Strategy	DownsampleSam.STRATEGY
java.lang.Boolean	FastqToSam.STRIP_UNPAIRED_MATE_NUMBER
boolean	CreateSequenceDictionary.TRUNCATE_NAMES_AT_WHITESPACE
boolean	MergeBamAlignment.UNMAP_CONTAMINANT_READS
java.io.File	MergeBamAlignment.UNMAPPED_BAM
java.io.File	SamToFastq.UNPAIRED_FASTQ
java.lang.String	CreateSequenceDictionary.URI
boolean	FastqToSam.USE_SEQUENTIAL_FASTQS
boolean	MergeSamFiles.USE_THREADING
boolean	ValidateSamFile.VALIDATE_INDEX
boolean	FilterSamReads.WRITE_READS_FILES

Uses of Option in picard.sam.markduplicates

Fields in picard.sam.markduplicates with annotations of type Option

Modifier and Type	Field and Description
java.lang.String	EstimateLibraryComplexity.BARCODE_TAG
java.lang.String	MarkDuplicates.BARCODE_TAG
int	MarkDuplicatesWithMateCigar.BLOCK_SIZE
java.util.List<java.io.File>	EstimateLibraryComplexity.INPUT
double	EstimateLibraryComplexity.MAX_DIFF_RATE
int	MarkDuplicates.MAX_FILE_HANDLES_FOR_READ_ENDS_MAP
int	EstimateLibraryComplexity.MAX_GROUP_RATIO
int	EstimateLibraryComplexity.MAX_READ_LENGTH
int	MarkDuplicates.MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP If more than this many sequences in SAM file, don't spill to disk because there will not be enough file handles.
int	EstimateLibraryComplexity.MIN_GROUP_COUNT
int	EstimateLibraryComplexity.MIN_IDENTICAL_BASES
int	EstimateLibraryComplexity.MIN_MEAN_QUALITY
int	MarkDuplicatesWithMateCigar.MINIMUM_DISTANCE
java.io.File	EstimateLibraryComplexity.OUTPUT
java.lang.String	EstimateLibraryComplexity.READ_ONE_BARCODE_TAG
java.lang.String	MarkDuplicates.READ_ONE_BARCODE_TAG
java.lang.String	EstimateLibraryComplexity.READ_TWO_BARCODE_TAG
java.lang.String	MarkDuplicates.READ_TWO_BARCODE_TAG
boolean	MarkDuplicates.REMOVE_SEQUENCING_DUPLICATES
double	MarkDuplicates.SORTING_COLLECTION_SIZE_RATIO
MarkDuplicates.DuplicateTaggingPolicy	MarkDuplicates.TAGGING_POLICY

Uses of Option in picard.sam.markduplicates.util

Fields in picard.sam.markduplicates.util with annotations of type Option

Modifier and Type	Field and Description
htsjdk.samtools.SAMFileHeader.SortOrder	AbstractMarkDuplicatesCommandLineProgram.ASSUME_SORT_ORDER
boolean	AbstractMarkDuplicatesCommandLineProgram.ASSUME_SORTED Deprecated.
java.util.List<java.lang.String>	AbstractMarkDuplicatesCommandLineProgram.COMMENT
htsjdk.samtools.DuplicateScoringStrategy.ScoringStrategy	AbstractMarkDuplicatesCommandLineProgram.DUPLICATE_SCORING_STRATEGY
java.util.List<java.lang.String>	AbstractMarkDuplicatesCommandLineProgram.INPUT
java.io.File	AbstractMarkDuplicatesCommandLineProgram.METRICS_FILE
int	AbstractOpticalDuplicateFinderCommandLineProgram.OPTICAL_DUPLICATE_PIXEL_DISTANCE
java.io.File	AbstractMarkDuplicatesCommandLineProgram.OUTPUT
java.lang.String	AbstractMarkDuplicatesCommandLineProgram.PROGRAM_GROUP_COMMAND_LINE
java.lang.String	AbstractMarkDuplicatesCommandLineProgram.PROGRAM_GROUP_NAME
java.lang.String	AbstractMarkDuplicatesCommandLineProgram.PROGRAM_GROUP_VERSION
java.lang.String	AbstractMarkDuplicatesCommandLineProgram.PROGRAM_RECORD_ID
java.lang.String	AbstractOpticalDuplicateFinderCommandLineProgram.READ_NAME_REGEX
boolean	AbstractMarkDuplicatesCommandLineProgram.REMOVE_DUPLICATES

Uses of Option in picard.util

Fields in picard.util with annotations of type Option

Modifier and Type	Field and Description
IntervalListTools.Action	IntervalListTools.ACTION
int	BaitDesigner.BAIT_OFFSET
int	BaitDesigner.BAIT_SIZE
int	IntervalListTools.BREAK_BANDS_AT_MULTIPLES_OF
int	FifoBuffer.BUFFER_SIZE
java.io.File	LiftOverIntervalList.CHAIN
java.util.List<java.lang.String>	IntervalListTools.COMMENT
int	FifoBuffer.DEBUG_FREQUENCY
java.lang.String	BaitDesigner.DESIGN_NAME
boolean	BaitDesigner.DESIGN_ON_TARGET_STRAND
BaitDesigner.DesignStrategy	BaitDesigner.DESIGN_STRATEGY
boolean	BaitDesigner.FILL_POOLS
boolean	IntervalListTools.INCLUDE_FILTERED
java.io.File	BedToIntervalList.INPUT
java.io.File	IntervalListToBed.INPUT
java.util.List<java.io.File>	IntervalListTools.INPUT
java.io.File	LiftOverIntervalList.INPUT
boolean	IntervalListTools.INVERT
int	FifoBuffer.IO_SIZE
java.lang.String	BaitDesigner.LEFT_PRIMER
int	ScatterIntervalsByNs.MAX_TO_MERGE
boolean	BaitDesigner.MERGE_NEARBY_TARGETS
double	LiftOverIntervalList.MIN_LIFTOVER_PCT
int	BaitDesigner.MINIMUM_BAITS_PER_TARGET
java.lang.String	FifoBuffer.NAME
java.io.File	BedToIntervalList.OUTPUT
java.io.File	IntervalListToBed.OUTPUT
java.io.File	IntervalListTools.OUTPUT
java.io.File	LiftOverIntervalList.OUTPUT
java.io.File	ScatterIntervalsByNs.OUTPUT
boolean	BaitDesigner.OUTPUT_AGILENT_FILES
java.io.File	BaitDesigner.OUTPUT_DIRECTORY
picard.util.ScatterIntervalsByNs.OutputType	ScatterIntervalsByNs.OUTPUT_TYPE
int	BaitDesigner.PADDING
int	IntervalListTools.PADDING
int	BaitDesigner.POOL_SIZE
java.io.File	ScatterIntervalsByNs.REFERENCE
java.io.File	BaitDesigner.REFERENCE_SEQUENCE
int	BaitDesigner.REPEAT_TOLERANCE
java.lang.String	BaitDesigner.RIGHT_PRIMER
int	IntervalListTools.SCATTER_COUNT
int	IntervalListToBed.SCORE
java.util.List<java.io.File>	IntervalListTools.SECOND_INPUT
java.io.File	BedToIntervalList.SEQUENCE_DICTIONARY
java.io.File	LiftOverIntervalList.SEQUENCE_DICTIONARY
boolean	BedToIntervalList.SORT
boolean	IntervalListToBed.SORT
boolean	IntervalListTools.SORT
IntervalListScatterer.Mode	IntervalListTools.SUBDIVISION_MODE
java.io.File	BaitDesigner.TARGETS
boolean	BedToIntervalList.UNIQUE
boolean	IntervalListTools.UNIQUE

Uses of Option in picard.vcf

Fields in picard.vcf with annotations of type Option

Modifier and Type	Field and Description
boolean	LiftoverVcf.ALLOW_MISSING_FIELDS_IN_HEADER
java.lang.String	GenotypeConcordance.CALL_SAMPLE
java.io.File	GenotypeConcordance.CALL_VCF
java.io.File	LiftoverVcf.CHAIN
java.io.File	CollectVariantCallingMetrics.DBSNP
boolean	CollectVariantCallingMetrics.GVCF_INPUT
java.io.File	SplitVcfs.INDEL_OUTPUT
java.io.File	CollectVariantCallingMetrics.INPUT
java.util.List<java.io.File>	GatherVcfs.INPUT
java.io.File	LiftoverVcf.INPUT
java.io.File	MakeSitesOnlyVcf.INPUT
java.util.List<java.io.File>	MergeVcfs.INPUT
java.io.File	RenameSampleInVcf.INPUT
java.util.List<java.io.File>	SortVcf.INPUT
java.io.File	SplitVcfs.INPUT
java.io.File	UpdateVcfSequenceDictionary.INPUT
java.io.File	VcfFormatConverter.INPUT
java.io.File	VcfToIntervalList.INPUT
boolean	GenotypeConcordance.INTERSECT_INTERVALS
java.util.List<java.io.File>	GenotypeConcordance.INTERVALS
double	LiftoverVcf.LIFTOVER_MIN_MATCH
int	GenotypeConcordance.MIN_DP
int	GenotypeConcordance.MIN_GQ
boolean	GenotypeConcordance.MISSING_SITES_HOM_REF
java.lang.String	RenameSampleInVcf.NEW_SAMPLE_NAME
java.lang.String	RenameSampleInVcf.OLD_SAMPLE_NAME
java.io.File	CollectVariantCallingMetrics.OUTPUT
java.io.File	GatherVcfs.OUTPUT
java.io.File	GenotypeConcordance.OUTPUT
java.io.File	LiftoverVcf.OUTPUT
java.io.File	MakeSitesOnlyVcf.OUTPUT
java.io.File	MergeVcfs.OUTPUT
java.io.File	RenameSampleInVcf.OUTPUT
java.io.File	SortVcf.OUTPUT
java.io.File	UpdateVcfSequenceDictionary.OUTPUT
java.io.File	VcfFormatConverter.OUTPUT
java.io.File	VcfToIntervalList.OUTPUT
boolean	GenotypeConcordance.OUTPUT_ALL_ROWS
java.io.File	LiftoverVcf.REFERENCE_SEQUENCE
java.io.File	LiftoverVcf.REJECT
java.lang.Boolean	VcfFormatConverter.REQUIRE_INDEX
java.util.Set<java.lang.String>	MakeSitesOnlyVcf.SAMPLE
java.io.File	CollectVariantCallingMetrics.SEQUENCE_DICTIONARY
java.io.File	MergeVcfs.SEQUENCE_DICTIONARY
java.io.File	SortVcf.SEQUENCE_DICTIONARY
java.io.File	SplitVcfs.SEQUENCE_DICTIONARY
java.io.File	UpdateVcfSequenceDictionary.SEQUENCE_DICTIONARY
java.io.File	SplitVcfs.SNP_OUTPUT
java.lang.Boolean	SplitVcfs.STRICT
java.io.File	CollectVariantCallingMetrics.TARGET_INTERVALS
int	CollectVariantCallingMetrics.THREAD_COUNT
java.lang.String	GenotypeConcordance.TRUTH_SAMPLE
java.io.File	GenotypeConcordance.TRUTH_VCF
boolean	GenotypeConcordance.USE_VCF_INDEX
boolean	LiftoverVcf.WARN_ON_MISSING_CONTIG
boolean	LiftoverVcf.WRITE_ORIGINAL_POSITION

Uses of Option in picard.vcf.filter

Fields in picard.vcf.filter with annotations of type Option

Modifier and Type	Field and Description
java.io.File	FilterVcf.INPUT
java.io.File	FilterVcf.JAVASCRIPT_FILE
double	FilterVcf.MAX_FS
double	FilterVcf.MIN_AB
int	FilterVcf.MIN_DP
int	FilterVcf.MIN_GQ
double	FilterVcf.MIN_QD
java.io.File	FilterVcf.OUTPUT