# Constant Field Values

## Contents

- picard.analysis.*
- picard.arrays.*
- picard.cmdline.*
- picard.fingerprint.*
- picard.illumina.*
- picard.metrics.*
- picard.sam.*
- picard.util.*
- picard.vcf.*

## picard.analysis.*

- picard.analysis.CollectInsertSizeMetrics
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `protected static final String` | `Histogram_R_SCRIPT` | `"picard/analysis/insertSizeHistogram.R"`

- picard.analysis.CollectRrbsMetrics
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final String` | `DETAIL_FILE_EXTENSION` | `"rrbs_detail_metrics"`
  `public static final String` | `PDF_FILE_EXTENSION` | `"rrbs_qc.pdf"`
  `public static final String` | `SUMMARY_FILE_EXTENSION` | `"rrbs_summary_metrics"`

- picard.analysis.artifacts.CollectSequencingArtifactMetrics
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final String` | `USAGE_SUMMARY` | `"Collect metrics to quantify single-base sequencing artifacts. "`

- picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final String` | `OXOG_METRICS_EXT` | `".oxog_metrics"`

- picard.analysis.artifacts.SequencingArtifactMetrics
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final String` | `BAIT_BIAS_DETAILS_EXT` | `".bait_bias_detail_metrics"`
  `public static final String` | `BAIT_BIAS_SUMMARY_EXT` | `".bait_bias_summary_metrics"`
  `public static final String` | `ERROR_SUMMARY_EXT` | `".error_summary_metrics"`
  `public static final String` | `PRE_ADAPTER_DETAILS_EXT` | `".pre_adapter_detail_metrics"`
  `public static final String` | `PRE_ADAPTER_SUMMARY_EXT` | `".pre_adapter_summary_metrics"`

- picard.analysis.directed.RnaSeqMetricsCollector
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final int` | `defaultEndBiasBases` | `100`

- picard.analysis.directed.TargetMetricsCollector<METRIC_TYPE extends MultilevelMetrics>
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final int` | `NEAR_PROBE_DISTANCE_DEFAULT` | `250`

## picard.arrays.*

- picard.arrays.CreateBafRegressMetricsFile
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final String` | `FILE_EXTENSION` | `"bafregress_metrics"`

- picard.arrays.CreateVerifyIDIntensityContaminationMetricsFile
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final String` | `FILE_EXTENSION` | `"verifyidintensity_metrics"`

- picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final String` | `ACGT_CODES` | `"ACGTacgt"`
  `public static final String` | `BUILD_37` | `"37"`
  `public static final int` | `FIVE_PRIME_SEQUENCE` | `1`
  `public static final int` | `INDEL_SEQUENCE` | `3`
  `public static final String` | `IUPAC_NUCLEOTIDE_CODES` | `"ACGTRYSWKMBDHVNacgtryswkmbdhvn"`
  `public static final int` | `PRE_INDEL_SEQUENCE` | `2`
  `public static final int` | `THREE_PRIME_SEQUENCE` | `4`

- picard.arrays.illumina.IlluminaManifest
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final String` | `ADDRESS_A_ID_HEADER_NAME` | `"AddressA_ID"`
  `public static final String` | `ADDRESS_B_ID_HEADER_NAME` | `"AddressB_ID"`
  `public static final String` | `ALLELE_A_PROBE_SEQ_HEADER_NAME` | `"AlleleA_ProbeSeq"`
  `public static final String` | `ALLELE_B_PROBE_SEQ_HEADER_NAME` | `"AlleleB_ProbeSeq"`
  `public static final String` | `BEAD_SET_ID_HEADER_NAME` | `"BeadSetID"`
  `public static final String` | `CHROMOSOME_HEADER_NAME` | `"Chr"`
  `public static final String` | `EXP_CLUSTERS_HEADER_NAME` | `"Exp_Clusters"`
  `public static final String` | `GENOME_BUILD_HEADER_NAME` | `"GenomeBuild"`
  `public static final String` | `HG17` | `"HG17"`
  `public static final String` | `HG18` | `"HG18"`
  `public static final String` | `HG19` | `"HG19"`
  `public static final String` | `ILLUMINA_ID_HEADER_NAME` | `"IlmnID"`
  `public static final String` | `ILLUMINA_STRAND_HEADER_NAME` | `"IlmnStrand"`
  `public static final String` | `INTENSITY_ONLY_HEADER_NAME` | `"Intensity_Only"`
  `public static final String` | `MAP_INFO_HEADER_NAME` | `"MapInfo"`
  `public static final String` | `NAME_HEADER_NAME` | `"Name"`
  `public static final String` | `NCBI_35` | `"35"`
  `public static final String` | `NCBI_36` | `"36"`
  `public static final String` | `NCBI_37` | `"37"`
  `public static final String` | `PLOIDY_HEADER_NAME` | `"Ploidy"`
  `public static final String` | `REF_STRAND_HEADER_NAME` | `"RefStrand"`
  `public static final String` | `SNP_HEADER_NAME` | `"SNP"`
  `public static final String` | `SOURCE_HEADER_NAME` | `"Source"`
  `public static final String` | `SOURCE_SEQ_HEADER_NAME` | `"SourceSeq"`
  `public static final String` | `SOURCE_STRAND_HEADER_NAME` | `"SourceStrand"`
  `public static final String` | `SOURCE_VERSION_HEADER_NAME` | `"SourceVersion"`
  `public static final String` | `SPECIES_HEADER_NAME` | `"Species"`
  `public static final String` | `TOP_GENOMIC_SEQ_HEADER_NAME` | `"TopGenomicSeq"`

- picard.arrays.illumina.IlluminaManifestRecord
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final String` | `ILLUMINA_FLAGGED_BAD_CHR` | `"0"`

- picard.arrays.illumina.InfiniumDataFile
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final int` | `MAX_UNSIGNED_SHORT` | `65535`

- picard.arrays.illumina.InfiniumEGTFile
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final String` | `EXTENSION` | `"egt"`

- picard.arrays.illumina.InfiniumGTCFile
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final byte` | `AA_CALL` | `1`
  `public static final byte` | `AB_CALL` | `2`
  `public static final byte` | `BB_CALL` | `3`
  `public static final byte` | `NO_CALL` | `0`

- picard.arrays.illumina.InfiniumVcfFields
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final String` | `ALLELE_A` | `"ALLELE_A"`
  `public static final String` | `ALLELE_B` | `"ALLELE_B"`
  `public static final String` | `ANALYSIS_VERSION_NUMBER` | `"analysisVersionNumber"`
  `public static final String` | `ARRAY_TYPE` | `"arrayType"`
  `public static final String` | `AUTOCALL_DATE` | `"autocallDate"`
  `public static final String` | `AUTOCALL_GENDER` | `"autocallGender"`
  `public static final String` | `AUTOCALL_VERSION` | `"autocallVersion"`
  `public static final String` | `BAF` | `"BAF"`
  `public static final String` | `BEADSET_ID` | `"BEADSET_ID"`
  `public static final String` | `CHIP_WELL_BARCODE` | `"chipWellBarcode"`
  `public static final String` | `CLUSTER_FILE` | `"clusterFile"`
  `public static final String` | `DUPE` | `"DUPE"`
  `public static final String` | `EXPECTED_GENDER` | `"expectedGender"`
  `public static final String` | `EXTENDED_ILLUMINA_MANIFEST_FILE` | `"extendedManifestFile"`
  `public static final String` | `EXTENDED_ILLUMINA_MANIFEST_VERSION` | `"extendedIlluminaManifestVersion"`
  `public static final String` | `FAIL_REF` | `"FAIL_REF"`
  `public static final String` | `FINGERPRINT_GENDER` | `"fingerprintGender"`
  `public static final String` | `GC_SCORE` | `"GC_SCORE"`
  `public static final String` | `GTA` | `"GTA"`
  `public static final String` | `GTC_CALL_RATE` | `"gtcCallRate"`
  `public static final String` | `GTC_CALL_RATE_DETAIL` | `"gtcCallRateDetail"`
  `public static final String` | `GTZ` | `"GTZ"`
  `public static final String` | `IGC` | `"IGC"`
  `public static final String` | `ILLUMINA_BUILD` | `"ILLUMINA_BUILD"`
  `public static final String` | `ILLUMINA_CHR` | `"ILLUMINA_CHR"`
  `public static final String` | `ILLUMINA_POS` | `"ILLUMINA_POS"`
  `public static final String` | `ILLUMINA_STRAND` | `"ILLUMINA_STRAND"`
  `public static final String` | `IMAGING_DATE` | `"imagingDate"`
  `public static final String` | `LRR` | `"LRR"`
  `public static final String` | `MANIFEST_FILE` | `"manifestFile"`
  `public static final String` | `NORMX` | `"NORMX"`
  `public static final String` | `NORMY` | `"NORMY"`
  `public static final String` | `P_95_GREEN` | `"p95Green"`
  `public static final String` | `P_95_RED` | `"p95Red"`
  `public static final String` | `PIPELINE_VERSION` | `"pipelineVersion"`
  `public static final String` | `PROBE_A` | `"PROBE_A"`
  `public static final String` | `PROBE_B` | `"PROBE_B"`
  `public static final String` | `R` | `"R"`
  `public static final String` | `RS_ID` | `"refSNP"`
  `public static final String` | `SAMPLE_ALIAS` | `"sampleAlias"`
  `public static final String` | `SCANNER_NAME` | `"scannerName"`
  `public static final String` | `SOURCE` | `"SOURCE"`
  `public static final String` | `THETA` | `"THETA"`
  `public static final String` | `TRIALLELIC` | `"TRIALLELIC"`
  `public static final String` | `X` | `"X"`
  `public static final String` | `Y` | `"Y"`
  `public static final String` | `ZCALL_THRESHOLDS` | `"zcallThresholds"`
  `public static final String` | `ZCALL_VERSION` | `"zcallVersion"`
  `public static final String` | `ZEROED_OUT_ASSAY` | `"ZEROED_OUT_ASSAY"`
  `public static final String` | `ZTHRESH_X` | `"zthresh_X"`
  `public static final String` | `ZTHRESH_Y` | `"zthresh_Y"`

## picard.cmdline.*

- picard.cmdline.StandardOptionDefinitions
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final String` | `ASSUME_SORT_ORDER_SHORT_NAME` | `"ASO"`
  `public static final String` | `ASSUME_SORTED_SHORT_NAME` | `"AS"`
  `public static final String` | `EXPECTED_INSERT_SIZE_SHORT_NAME` | `"INSERT"`
  `public static final String` | `INPUT_SHORT_NAME` | `"I"`
  `public static final String` | `LANE_SHORT_NAME` | `"L"`
  `public static final String` | `LIBRARY_NAME_SHORT_NAME` | `"LIB"`
  `public static final String` | `METRICS_FILE_SHORT_NAME` | `"M"`
  `public static final String` | `MINIMUM_LOD_SHORT_NAME` | `"LOD"`
  `public static final String` | `MINIMUM_MAPPING_QUALITY_SHORT_NAME` | `"MQ"`
  `public static final String` | `OUTPUT_SHORT_NAME` | `"O"`
  `public static final String` | `PF_READS_ONLY_SHORT_NAME` | `"PF"`
  `public static final String` | `PROGRAM_RECORD_ID_SHORT_NAME` | `"PG"`
  `public static final String` | `READ_GROUP_ID_SHORT_NAME` | `"RG"`
  `public static final String` | `REFERENCE_SHORT_NAME` | `"R"`
  `public static final String` | `SAMPLE_ALIAS_SHORT_NAME` | `"ALIAS"`
  `public static final String` | `SEQUENCE_DICTIONARY_SHORT_NAME` | `"SD"`
  `public static final String` | `SORT_ORDER_SHORT_NAME` | `"SO"`
  `public static final String` | `USE_ORIGINAL_QUALITIES_SHORT_NAME` | `"OQ"`

## picard.fingerprint.*

- picard.fingerprint.CalculateFingerprintMetrics
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public final double` | `GENOTYPE_LOD_THRESHOLD` | `3.0`
  `public final int` | `NUMBER_OF_SAMPLING` | `100`

- picard.fingerprint.CheckFingerprint
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final String` | `FINGERPRINT_DETAIL_FILE_SUFFIX` | `"fingerprinting_detail_metrics"`
  `public static final String` | `FINGERPRINT_SUMMARY_FILE_SUFFIX` | `"fingerprinting_summary_metrics"`

- picard.fingerprint.FingerprintChecker
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final double` | `DEFAULT_GENOTYPING_ERROR_RATE` | `0.01`
  `public static final int` | `DEFAULT_MINIMUM_BASE_QUALITY` | `20`
  `public static final int` | `DEFAULT_MINIMUM_MAPPING_QUALITY` | `10`

- picard.fingerprint.HaplotypeMap
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final String` | `HET_GENOTYPE_FOR_PHASING` | `"HetGenotypeForPhasing"`
  `public static final String` | `PHASESET_PREFIX` | `"PhaseSet"`
  `public static final String` | `SYNTHETIC_PHASESET_PREFIX` | `"Synthetic"`

- picard.fingerprint.LiftOverHaplotypeMap
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final int` | `LIFTOVER_FAILED_FOR_ONE_OR_MORE_SNPS` | `101`

## picard.illumina.*

- picard.illumina.ExtractBarcodesProgram
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final String` | `BARCODE_COLUMN` | `"barcode"`
  `public static final String` | `BARCODE_NAME_COLUMN` | `"barcode_name"`
  `public static final String` | `BARCODE_SEQUENCE_COLUMN` | `"barcode_sequence"`
  `public static final String` | `LIBRARY_NAME_COLUMN` | `"library_name"`

- picard.illumina.IlluminaBasecallsToSam
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final String` | `USAGE` | `"Generate a SAM, BAM or CRAM file from data in an Illumina basecalls output directory"`

- picard.illumina.parser.MultiTileBclParser
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final byte` | `MASKING_QUALITY` | `2`

- picard.illumina.parser.ParameterizedFileUtil
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `protected static final boolean` | `DefaultSkipEmptyFiles` | `true`
  `public static final String` | `PER_TILE_PATTERN_STRING` | `"s_(\\d+)_(\\d{1,5})"`

- picard.illumina.parser.ReadStructure
  Modifier and Type | Constant Field | Value
  --- | --- | ---

  `public static final String`

  `PARAMETER_DOC`

  `"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."`

- picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final float` | `MAX_POS` | `1.0E7f`
  `public static final float` | `MIN_POS` | `-10.0f`
  `public static final String` | `S_LOCS_FILE` | `"s.locs"`

- picard.illumina.parser.readers.BaseBclReader
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final byte` | `NO_CALL_BASE` | `78`

- picard.illumina.parser.readers.BclQualityEvaluationStrategy
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final int` | `ILLUMINA_ALLEGED_MINIMUM_QUALITY` | `2`

- picard.illumina.parser.readers.FilterFileReader
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final int` | `EXPECTED_VERSION` | `3`

- picard.illumina.quality.CollectHiSeqXPfFailMetrics
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final String` | `detailedMetricsExtension` | `".pffail_detailed_metrics"`
  `public static final String` | `summaryMetricsExtension` | `".pffail_summary_metrics"`

## picard.metrics.*

- picard.metrics.MultiLevelCollector<METRIC_TYPE extends htsjdk.samtools.metrics.MetricBase,​Histogram_KEY extends Comparable,​ARGTYPE>
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final String` | `UNKNOWN` | `"unknown"`

## picard.sam.*

- picard.sam.AbstractAlignmentMerger
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final int` | `MAX_RECORDS_IN_RAM` | `500000`

- picard.sam.AddOrReplaceReadGroups
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final String` | `READGROUP_ID_REGEX` | `"^[ -~]+$"`

- picard.sam.DownsampleSam
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final String` | `RANDOM_SEED_TAG` | `"rs"`

- picard.sam.SplitSamByLibrary
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final int` | `NO_LIBRARIES_SPECIFIED_IN_HEADER` | `2`

- picard.sam.markduplicates.MarkDuplicates
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final String` | `DUPLICATE_SET_INDEX_TAG` | `"DI"`
  `public static final String` | `DUPLICATE_SET_SIZE_TAG` | `"DS"`
  `public static final String` | `DUPLICATE_TYPE_LIBRARY` | `"LB"`
  `public static final String` | `DUPLICATE_TYPE_SEQUENCING` | `"SQ"`
  `public static final String` | `DUPLICATE_TYPE_TAG` | `"DT"`

- picard.sam.markduplicates.util.OpticalDuplicateFinder
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final int` | `DEFAULT_BIG_DUPLICATE_SET_SIZE` | `1000`
  `public static final int` | `DEFAULT_MAX_DUPLICATE_SET_SIZE` | `300000`
  `public static final int` | `DEFAULT_OPTICAL_DUPLICATE_DISTANCE` | `100`

- picard.sam.markduplicates.util.ReadEnds
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final byte` | `F` | `0`
  `public static final byte` | `FF` | `2`
  `public static final byte` | `FR` | `3`
  `public static final byte` | `R` | `1`
  `public static final byte` | `RF` | `5`
  `public static final byte` | `RR` | `4`

- picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `protected static final int` | `SIZE_OF` | `69`

- picard.sam.SamErrorMetric.ReadBaseStratification
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final int` | `NOT_ALIGNED_ERROR` | `-1`

- picard.sam.util.PhysicalLocation
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final int` | `NO_VALUE` | `-1`

## picard.util.*

- picard.util.AdapterMarker
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final int` | `DEFAULT_ADAPTER_LENGTH` | `30`
  `public static final int` | `DEFAULT_NUM_ADAPTERS_TO_KEEP` | `1`
  `public static final int` | `DEFAULT_PRUNE_ADAPTER_LIST_AFTER_THIS_MANY_ADAPTERS_SEEN` | `100`

- picard.util.AsyncIterator<T>
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final int` | `DEFAULT_QUEUE_SIZE` | `2000`

- picard.util.ClippingUtility
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final double` | `MAX_ERROR_RATE` | `0.1`
  `public static final double` | `MAX_PE_ERROR_RATE` | `0.1`
  `public static final int` | `MIN_MATCH_BASES` | `12`
  `public static final int` | `MIN_MATCH_PE_BASES` | `6`
  `public static final int` | `NO_MATCH` | `-1`

- picard.util.IlluminaUtil
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final String` | `BARCODE_DELIMITER` | `"-"`

- picard.util.LiftoverUtils
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final String` | `REV_COMPED_ALLELES` | `"ReverseComplementedAlleles"`
  `public static final String` | `SWAPPED_ALLELES` | `"SwappedAlleles"`

- picard.util.MathUtil
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final double` | `MAX_PROB_BELOW_ONE` | `0.9999999999999999`

- picard.util.help.HelpConstants
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final String` | `DOC_CAT_BASE_CALLING` | `"Base Calling"`
  `public static final String` | `DOC_CAT_BASE_CALLING_SUMMARY` | `"Tools that process sequencing machine data, e.g. Illumina base calls, and detect sequencing level attributes, e.g. adapters"`
  `public static final String` | `DOC_CAT_DIAGNOSTICS_AND_QC` | `"Diagnostics and Quality Control"`
  `public static final String` | `DOC_CAT_DIAGNOSTICS_AND_QC_SUMMARY` | `"Tools that collect sequencing quality related and comparative metrics"`
  `public static final String` | `DOC_CAT_GENOTYPING_ARRAYS_MANIPULATION` | `"Genotyping Arrays Manipulation"`
  `public static final String` | `DOC_CAT_GENOTYPING_ARRAYS_MANIPULATION_SUMMARY` | `"Tools that manipulate data generated by Genotyping arrays"`
  `public static final String` | `DOC_CAT_INTERVALS_MANIPULATION` | `"Intervals Manipulation"`
  `public static final String` | `DOC_CAT_INTERVALS_MANIPULATION_SUMMARY` | `"Tools that process genomic intervals in various formats"`
  `public static final String` | `DOC_CAT_OTHER` | `"Other"`
  `public static final String` | `DOC_CAT_OTHER_SUMMARY` | `"Miscellaneous tools, e.g. those that aid in data streaming"`
  `public static final String` | `DOC_CAT_READ_DATA_MANIPULATION` | `"Read Data Manipulation"`
  `public static final String` | `DOC_CAT_READ_DATA_MANIPULATION_SUMMARY` | `"Tools that manipulate read data in SAM, BAM or CRAM format"`
  `public static final String` | `DOC_CAT_REFERENCE` | `"Reference"`
  `public static final String` | `DOC_CAT_REFERENCE_SUMMARY` | `"Tools that analyze and manipulate FASTA format references"`
  `public static final String` | `DOC_CAT_TEST` | `"Test Tools"`
  `public static final String` | `DOC_CAT_TEST_SUMMARY` | `"Tools for internal test purposes"`
  `public static final String` | `DOC_CAT_VARIANT_EVALUATION` | `"Variant Evaluation and Refinement"`
  `public static final String` | `DOC_CAT_VARIANT_EVALUATION_SUMMARY` | `"Tools that evaluate and refine variant calls, e.g. with annotations not offered by the engine"`
  `public static final String` | `DOC_CAT_VARIANT_FILTERING` | `"Variant Filtering"`
  `public static final String` | `DOC_CAT_VARIANT_FILTERING_SUMMARY` | `"Tools that filter variants by annotating the FILTER column"`
  `public static final String` | `DOC_CAT_VARIANT_MANIPULATION` | `"Variant Manipulation"`
  `public static final String` | `DOC_CAT_VARIANT_MANIPULATION_SUMMARY` | `"Tools that manipulate variant call format (VCF) data"`
  `public static final String` | `DOC_SUPERCAT_EXCLUDE` | `"exclude"`
  `public static final String` | `DOC_SUPERCAT_TOOLS` | `"tools"`
  `public static final String` | `DOC_SUPERCAT_UTILITIES` | `"utilities"`

## picard.vcf.*

- picard.vcf.GenotypeConcordance
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final String` | `CONTINGENCY_METRICS_FILE_EXTENSION` | `".genotype_concordance_contingency_metrics"`
  `public static final String` | `CONTINGENCY_STATE_TAG` | `"CONC_ST"`
  `public static final String` | `DETAILED_METRICS_FILE_EXTENSION` | `".genotype_concordance_detail_metrics"`
  `public static final String` | `OUTPUT_VCF_CALL_SAMPLE_NAME` | `"call"`
  `public static final String` | `OUTPUT_VCF_FILE_EXTENSION` | `".genotype_concordance.vcf.gz"`
  `public static final String` | `OUTPUT_VCF_TRUTH_SAMPLE_NAME` | `"truth"`
  `public static final String` | `SUMMARY_METRICS_FILE_EXTENSION` | `".genotype_concordance_summary_metrics"`

- picard.vcf.LiftoverVcf
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final String` | `ATTEMPTED_ALLELES` | `"AttemptedAlleles"`
  `public static final String` | `ATTEMPTED_LOCUS` | `"AttemptedLocus"`
  `public static final String` | `FILTER_CANNOT_LIFTOVER_REV_COMP` | `"CannotLiftOver"`
  `public static final String` | `FILTER_INDEL_STRADDLES_TWO_INTERVALS` | `"IndelStraddlesMultipleIntevals"`
  `public static final String` | `FILTER_MISMATCHING_REF_ALLELE` | `"MismatchedRefAllele"`
  `public static final String` | `FILTER_NO_TARGET` | `"NoTarget"`
  `public static final String` | `ORIGINAL_ALLELES` | `"OriginalAlleles"`
  `public static final String` | `ORIGINAL_CONTIG` | `"OriginalContig"`
  `public static final String` | `ORIGINAL_START` | `"OriginalStart"`

- picard.vcf.VcfToIntervalList
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final String` | `INCLUDE_FILTERED_SHORT_NAME` | `"IF"`

- picard.vcf.filter.AlleleBalanceFilter
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final String` | `AB_FILTER` | `"AlleleBalance"`

- picard.vcf.filter.FilterApplyingVariantIterator
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final String` | `ALL_GTS_FILTERED` | `"AllGtsFiltered"`
  `public static final String` | `PASS_FILTER` | `"PASS"`

- picard.vcf.filter.QdFilter
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final String` | `FILTER_NAME` | `"LowQD"`