Constant Field Values

Contents

• org.broadinstitute.*
• picard.analysis.*
• picard.arrays.*
• picard.cmdline.*
• picard.fingerprint.*
• picard.illumina.*
• picard.metrics.*
• picard.sam.*
• picard.util.*
• picard.vcf.*

org.broadinstitute.*

org.broadinstitute.hellbender.Main

Modifier and Type	Constant Field	Value
public static final int	PICARD_TOOL_EXCEPTION	4
public static final int	USER_EXCEPTION_EXIT_VALUE	2

org.broadinstitute.hellbender.cmdline.ExomeStandardArgumentDefinitions

Modifier and Type	Constant Field	Value
public static final java.lang.String	AF_PARAMETER_FILE_LONG_NAME	"paramAF"
public static final java.lang.String	AF_PARAMETER_FILE_SHORT_NAME	"AF"
public static final java.lang.String	ALLELIC_COUNTS_FILE_LONG_NAME	"hets"
public static final java.lang.String	ALLELIC_COUNTS_FILE_SHORT_NAME	"HET"
public static final java.lang.String	ALLELIC_PON_FILE_LONG_NAME	"allelicPanelOfNormals"
public static final java.lang.String	ALLELIC_PON_FILE_SHORT_NAME	"aPON"
public static final java.lang.String	BAITS_FILE_LONG_NAME	"baits"
public static final java.lang.String	BAITS_FILE_SHORT_NAME	"B"
public static final java.lang.String	LEGACY_SEG_FILE_LONG_NAME	"legacy"
public static final java.lang.String	LEGACY_SEG_FILE_SHORT_NAME	"LEG"
public static final java.lang.String	LOG2_LONG_NAME	"log2Input"
public static final java.lang.String	LOG2_SHORT_NAME	"LOG"
public static final java.lang.String	NORMAL_ALLELIC_COUNTS_FILE_LONG_NAME	"normalHets"
public static final java.lang.String	NORMAL_ALLELIC_COUNTS_FILE_SHORT_NAME	"NHET"
public static final java.lang.String	NORMAL_BAM_FILE_LONG_NAME	"normal"
public static final java.lang.String	NORMAL_BAM_FILE_SHORT_NAME	"N"
public static final java.lang.String	PON_FILE_LONG_NAME	"panelOfNormals"
public static final java.lang.String	PON_FILE_SHORT_NAME	"PON"
public static final java.lang.String	PRE_TANGENT_NORMALIZED_COUNTS_FILE_LONG_NAME	"preTangentNormalized"
public static final java.lang.String	PRE_TANGENT_NORMALIZED_COUNTS_FILE_SHORT_NAME	"PTN"
public static final java.lang.String	SEGMENT_FILE_LONG_NAME	"segments"
public static final java.lang.String	SEGMENT_FILE_SHORT_NAME	"S"
public static final java.lang.String	SITES_FILE_LONG_NAME	"siteIntervals"
public static final java.lang.String	SITES_FILE_SHORT_NAME	"SITES"
public static final java.lang.String	SNP_FILE_LONG_NAME	"snpIntervals"
public static final java.lang.String	SNP_FILE_SHORT_NAME	"SNP"
public static final java.lang.String	TANGENT_NORMALIZED_COUNTS_FILE_LONG_NAME	"tangentNormalized"
public static final java.lang.String	TANGENT_NORMALIZED_COUNTS_FILE_SHORT_NAME	"TN"
public static final java.lang.String	TARGET_FILE_LONG_NAME	"targets"
public static final java.lang.String	TARGET_FILE_SHORT_NAME	"T"
public static final java.lang.String	TUMOR_ALLELIC_COUNTS_FILE_LONG_NAME	"tumorHets"
public static final java.lang.String	TUMOR_ALLELIC_COUNTS_FILE_SHORT_NAME	"THET"
public static final java.lang.String	TUMOR_BAM_FILE_LONG_NAME	"tumor"
public static final java.lang.String	TUMOR_BAM_FILE_SHORT_NAME	"T"

org.broadinstitute.hellbender.cmdline.ReadFilterArgumentDefinitions

Modifier and Type	Constant Field	Value
public static final java.lang.String	AMBIGUOUS_FILTER_BASES_NAME	"ambig-filter-bases"
public static final java.lang.String	AMBIGUOUS_FILTER_FRACTION_NAME	"ambig-filter-frac"
public static final java.lang.String	BLACK_LISTED_LANES_LONG_NAME	"black-listed-lanes"
public static final java.lang.String	DISABLE_READ_FILTER_LONG_NAME	"disable-read-filter"
public static final java.lang.String	DISABLE_READ_FILTER_SHORT_NAME	"DF"
public static final java.lang.String	DISABLE_TOOL_DEFAULT_READ_FILTERS	"disable-tool-default-read-filters"
public static final java.lang.String	DONT_REQUIRE_SOFT_CLIPS_BOTH_ENDS_NAME	"dont-require-soft-clips-both-ends"
public static final java.lang.String	FILTER_TOO_SHORT_NAME	"filter-too-short"
public static final java.lang.String	INVERT_SOFT_CLIP_RATIO_FILTER	"invert-soft-clip-ratio-filter"
public static final java.lang.String	KEEP_INTERVAL_NAME	"keep-intervals"
public static final java.lang.String	KEEP_READ_GROUP_LONG_NAME	"keep-read-group"
public static final java.lang.String	KEEP_REVERSE_STRAND_ONLY_NAME	"keep-reverse-strand-only"
public static final java.lang.String	LIBRARY_NAME	"library"
public static final java.lang.String	MATE_TOO_DISTANT_LENGTH	"mate-too-distant-length"
public static final java.lang.String	MAX_FRAGMENT_LENGTH_NAME	"max-fragment-length"
public static final java.lang.String	MAX_READ_LENGTH_ARG_NAME	"max-read-length"
public static final java.lang.String	MAXIMUM_MAPPING_QUALITY_NAME	"maximum-mapping-quality"
public static final java.lang.String	MIN_FRAGMENT_LENGTH_NAME	"min-fragment-length"
public static final java.lang.String	MIN_READ_LENGTH_ARG_NAME	"min-read-length"
public static final java.lang.String	MINIMUM_MAPPING_QUALITY_NAME	"minimum-mapping-quality"
public static final java.lang.String	PL_FILTER_NAME_LONG_NAME	"platform-filter-name"
public static final java.lang.String	READ_FILTER_LONG_NAME	"read-filter"
public static final java.lang.String	READ_FILTER_SHORT_NAME	"RF"
public static final java.lang.String	READ_GROUP_BLACK_LIST_LONG_NAME	"read-group-black-list"
public static final java.lang.String	READ_NAME_LONG_NAME	"read-name"
public static final java.lang.String	SAMPLE_NAME	"sample"
public static final java.lang.String	SOFT_CLIPPED_LEADING_TRAILING_RATIO_THRESHOLD	"soft-clipped-leading-trailing-ratio"
public static final java.lang.String	SOFT_CLIPPED_RATIO_THRESHOLD	"soft-clipped-ratio-threshold"

org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions

Modifier and Type	Constant Field	Value
public static final java.lang.String	ADD_OUTPUT_SAM_PROGRAM_RECORD	"add-output-sam-program-record"
public static final java.lang.String	ADD_OUTPUT_VCF_COMMANDLINE	"add-output-vcf-command-line"
public static final java.lang.String	ANNOTATION_GROUP_LONG_NAME	"annotation-group"
public static final java.lang.String	ANNOTATION_GROUP_SHORT_NAME	"G"
public static final java.lang.String	ANNOTATION_LONG_NAME	"annotation"
public static final java.lang.String	ANNOTATION_SHORT_NAME	"A"
public static final java.lang.String	ANNOTATIONS_TO_EXCLUDE_LONG_NAME	"annotations-to-exclude"
public static final java.lang.String	ANNOTATIONS_TO_EXCLUDE_SHORT_NAME	"AX"
public static final java.lang.String	ASSUME_SORTED_LONG_NAME	"assume-sorted"
public static final java.lang.String	ASSUME_SORTED_SHORT_NAME	"AS"
public static final java.lang.String	BQSR_TABLE_LONG_NAME	"bqsr-recal-file"
public static final java.lang.String	BQSR_TABLE_SHORT_NAME	"bqsr"
public static final java.lang.String	CLOUD_INDEX_PREFETCH_BUFFER_LONG_NAME	"cloud-index-prefetch-buffer"
public static final java.lang.String	CLOUD_INDEX_PREFETCH_BUFFER_SHORT_NAME	"CIPB"
public static final java.lang.String	CLOUD_PREFETCH_BUFFER_LONG_NAME	"cloud-prefetch-buffer"
public static final java.lang.String	CLOUD_PREFETCH_BUFFER_SHORT_NAME	"CPB"
public static final java.lang.String	COMPARISON_LONG_NAME	"comparison"
public static final java.lang.String	COMPARISON_SHORT_NAME	"comp"
public static final java.lang.String	CREATE_OUTPUT_BAM_INDEX_LONG_NAME	"create-output-bam-index"
public static final java.lang.String	CREATE_OUTPUT_BAM_INDEX_SHORT_NAME	"OBI"
public static final java.lang.String	CREATE_OUTPUT_BAM_MD5_LONG_NAME	"create-output-bam-md5"
public static final java.lang.String	CREATE_OUTPUT_BAM_MD5_SHORT_NAME	"OBM"
public static final java.lang.String	CREATE_OUTPUT_VARIANT_INDEX_LONG_NAME	"create-output-variant-index"
public static final java.lang.String	CREATE_OUTPUT_VARIANT_INDEX_SHORT_NAME	"OVI"
public static final java.lang.String	CREATE_OUTPUT_VARIANT_MD5_LONG_NAME	"create-output-variant-md5"
public static final java.lang.String	CREATE_OUTPUT_VARIANT_MD5_SHORT_NAME	"OVM"
public static final java.lang.String	DISABLE_BAM_INDEX_CACHING_LONG_NAME	"disable-bam-index-caching"
public static final java.lang.String	DISABLE_BAM_INDEX_CACHING_SHORT_NAME	"DBIC"
public static final java.lang.String	DISABLE_SEQUENCE_DICT_VALIDATION_NAME	"disable-sequence-dictionary-validation"
public static final java.lang.String	DISABLE_TOOL_DEFAULT_ANNOTATIONS	"disable-tool-default-annotations"
public static final java.lang.String	DUPLICATE_SCORING_STRATEGY_LONG_NAME	"duplicate-scoring-strategy"
public static final java.lang.String	DUPLICATE_SCORING_STRATEGY_SHORT_NAME	"DS"
public static final java.lang.String	ENABLE_ALL_ANNOTATIONS	"enable-all-annotations"
public static final java.lang.String	FEATURE_LONG_NAME	"feature"
public static final java.lang.String	FEATURE_SHORT_NAME	"F"
public static final java.lang.String	GATK_CONFIG_FILE_OPTION	"gatk-config-file"
public static final java.lang.String	INPUT_INDEX_COMPANION	"inputIndex"
public static final java.lang.String	INPUT_LONG_NAME	"input"
public static final java.lang.String	INPUT_SHORT_NAME	"I"
public static final java.lang.String	INTERVALS_LONG_NAME	"intervals"
public static final java.lang.String	INTERVALS_SHORT_NAME	"L"
public static final java.lang.String	INVALIDATE_PREVIOUS_FILTERS_LONG_NAME	"invalidate-previous-filters"
public static final java.lang.String	LENIENT_LONG_NAME	"lenient"
public static final java.lang.String	LENIENT_SHORT_NAME	"LE"
public static final java.lang.String	MAX_VARIANTS_PER_SHARD_LONG_NAME	"max-variants-per-shard"
public static final java.lang.String	METRIC_ACCUMULATION_LEVEL_LONG_NAME	"metric-accumulation-level"
public static final java.lang.String	METRIC_ACCUMULATION_LEVEL_SHORT_NAME	"LEVEL"
public static final java.lang.String	METRICS_FILE_LONG_NAME	"metrics-file"
public static final java.lang.String	METRICS_FILE_SHORT_NAME	"M"
public static final java.lang.String	NIO_MAX_REOPENS_LONG_NAME	"gcs-max-retries"
public static final java.lang.String	NIO_MAX_REOPENS_SHORT_NAME	"gcs-retries"
public static final java.lang.String	NIO_PROJECT_FOR_REQUESTER_PAYS_LONG_NAME	"gcs-project-for-requester-pays"
public static final java.lang.String	OUTPUT_INDEX_COMPANION	"outputIndex"
public static final java.lang.String	OUTPUT_LONG_NAME	"output"
public static final java.lang.String	OUTPUT_SHORT_NAME	"O"
public static final java.lang.String	PEDIGREE_FILE_LONG_NAME	"pedigree"
public static final java.lang.String	PEDIGREE_FILE_SHORT_NAME	"ped"
public static final java.lang.String	PROGRAM_RECORD_ID_SHORT_NAME	"PG"
public static final java.lang.String	QUIET_NAME	"QUIET"
public static final java.lang.String	READ_INDEX_LONG_NAME	"read-index"
public static final java.lang.String	READ_INDEX_SHORT_NAME	"read-index"
public static final java.lang.String	READ_VALIDATION_STRINGENCY_LONG_NAME	"read-validation-stringency"
public static final java.lang.String	READ_VALIDATION_STRINGENCY_SHORT_NAME	"VS"
public static final java.lang.String	REFERENCE_DICTIONARY_COMPANION	"referenceDictionary"
public static final java.lang.String	REFERENCE_INDEX_COMPANION	"referenceIndex"
public static final java.lang.String	REFERENCE_LONG_NAME	"reference"
public static final java.lang.String	REFERENCE_SHORT_NAME	"R"
public static final java.lang.String	RESOURCE_LONG_NAME	"resource"
public static final java.lang.String	SAMPLE_ALIAS_SHORT_NAME	"ALIAS"
public static final java.lang.String	SAMPLE_NAME_LONG_NAME	"sample-name"
public static final java.lang.String	SAMPLE_NAME_SHORT_NAME	"sn"
public static final java.lang.String	SEQUENCE_DICTIONARY_NAME	"sequence-dictionary"
public static final java.lang.String	SITES_ONLY_LONG_NAME	"sites-only-vcf-output"
public static final java.lang.String	SORT_ORDER_LONG_NAME	"sort-order"
public static final java.lang.String	SORT_ORDER_SHORT_NAME	"SO"
public static final java.lang.String	SPARK_PROPERTY_NAME	"conf"
public static final java.lang.String	TMP_DIR_NAME	"tmp-dir"
public static final java.lang.String	USE_JDK_DEFLATER_LONG_NAME	"use-jdk-deflater"
public static final java.lang.String	USE_JDK_DEFLATER_SHORT_NAME	"jdk-deflater"
public static final java.lang.String	USE_JDK_INFLATER_LONG_NAME	"use-jdk-inflater"
public static final java.lang.String	USE_JDK_INFLATER_SHORT_NAME	"jdk-inflater"
public static final java.lang.String	USE_ORIGINAL_QUALITIES_LONG_NAME	"use-original-qualities"
public static final java.lang.String	USE_ORIGINAL_QUALITIES_SHORT_NAME	"OQ"
public static final java.lang.String	VARIANT_LONG_NAME	"variant"
public static final java.lang.String	VARIANT_SHORT_NAME	"V"
public static final java.lang.String	VERBOSITY_NAME	"verbosity"

org.broadinstitute.hellbender.cmdline.argumentcollections.DbsnpArgumentCollection

Modifier and Type	Constant Field	Value
public static final java.lang.String	DBSNP_LONG_NAME	"dbsnp"
public static final java.lang.String	DBSNP_SHORT_NAME	"D"

org.broadinstitute.hellbender.cmdline.argumentcollections.IntervalArgumentCollection

Modifier and Type	Constant Field	Value
public static final java.lang.String	EXCLUDE_INTERVALS_LONG_NAME	"exclude-intervals"
public static final java.lang.String	EXCLUDE_INTERVALS_SHORT_NAME	"XL"
public static final java.lang.String	INTERVAL_EXCLUSION_PADDING_LONG_NAME	"interval-exclusion-padding"
public static final java.lang.String	INTERVAL_MERGING_RULE_LONG_NAME	"interval-merging-rule"
public static final java.lang.String	INTERVAL_PADDING_LONG_NAME	"interval-padding"
public static final java.lang.String	INTERVAL_SET_RULE_LONG_NAME	"interval-set-rule"

org.broadinstitute.hellbender.cmdline.argumentcollections.MarkDuplicatesSparkArgumentCollection

Modifier and Type	Constant Field	Value
public static final java.lang.String	DO_NOT_MARK_UNMAPPED_MATES_LONG_NAME	"do-not-mark-unmapped-mates"
public static final java.lang.String	DUPLICATE_TAGGING_POLICY_LONG_NAME	"duplicate-tagging-policy"
public static final java.lang.String	REMOVE_ALL_DUPLICATE_READS	"remove-all-duplicates"
public static final java.lang.String	REMOVE_SEQUENCING_DUPLICATE_READS	"remove-sequencing-duplicates"

org.broadinstitute.hellbender.cmdline.argumentcollections.OpticalDuplicatesArgumentCollection

Modifier and Type	Constant Field	Value
public static final java.lang.String	OPTICAL_DUPLICATE_PIXEL_DISTANCE_LONG_NAME	"optical-duplicate-pixel-distance"
public static final java.lang.String	READ_NAME_REGEX_LONG_NAME	"read-name-regex"

org.broadinstitute.hellbender.engine.AbstractConcordanceWalker

Modifier and Type	Constant Field	Value
public static final int	CACHE_LOOKAHEAD	100000
public static final java.lang.String	CONFIDENCE_REGION_LONG_NAME	"confidence"
public static final java.lang.String	CONFIDENCE_REGION_SHORT_NAME	"C"
public static final java.lang.String	EVAL_VARIANTS_LONG_NAME	"evaluation"
public static final java.lang.String	EVAL_VARIANTS_SHORT_NAME	"eval"
public static final java.lang.String	TRUTH_VARIANTS_LONG_NAME	"truth"

org.broadinstitute.hellbender.engine.DuplicateSetWalker

Modifier and Type	Constant Field	Value
public static final java.lang.String	MIN_REQUIRED_READS_NAME	"min-reads"
public static final java.lang.String	MIN_REQUIRED_READS_PER_STRAND_NAME	"min-per-strand-reads"

org.broadinstitute.hellbender.engine.FeatureDataSource<T extends htsjdk.tribble.Feature>

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_QUERY_LOOKAHEAD_BASES	1000

org.broadinstitute.hellbender.engine.FeatureInput<T extends htsjdk.tribble.Feature>

Modifier and Type	Constant Field	Value
public static final java.lang.String	FEATURE_ARGUMENT_TAG_DELIMITER	":"

org.broadinstitute.hellbender.engine.GATKPath

Modifier and Type	Constant Field	Value
public static final java.lang.String	HDFS_SCHEME	"hdfs"

org.broadinstitute.hellbender.engine.GATKTool

Modifier and Type	Constant Field	Value
public static final java.lang.String	SECONDS_BETWEEN_PROGRESS_UPDATES_NAME	"seconds-between-progress-updates"

org.broadinstitute.hellbender.engine.LocusWalker

Modifier and Type	Constant Field	Value
public static final java.lang.String	MAX_DEPTH_PER_SAMPLE_NAME	"max-depth-per-sample"

org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart

Modifier and Type	Constant Field	Value
public static final java.lang.String	COMBINE_VARIANTS_DISTANCE	"combine-variants-distance"
public static final java.lang.String	IGNORE_VARIANTS_THAT_START_OUTSIDE_INTERVAL	"ignore-variants-starting-outside-interval"
public static final java.lang.String	MAX_COMBINED_DISTANCE	"max-distance"
public static final java.lang.String	REFERENCE_WINDOW_PADDING	"ref-padding"

org.broadinstitute.hellbender.engine.ProgressMeter

Modifier and Type	Constant Field	Value
public static final java.lang.String	DEFAULT_RECORD_LABEL	"records"
public static final long	DEFAULT_RECORDS_BETWEEN_TIME_CHECKS	1000L
public static final double	DEFAULT_SECONDS_BETWEEN_UPDATES	10.0
public static final long	MILLISECONDS_PER_MINUTE	60000L
public static final long	MILLISECONDS_PER_SECOND	1000L

org.broadinstitute.hellbender.engine.ReadWalker

Modifier and Type	Constant Field	Value
public static final int	FEATURE_CACHE_LOOKAHEAD	1000

org.broadinstitute.hellbender.engine.ReferenceShard

Modifier and Type	Constant Field	Value
public static final int	REFERENCE_SHARD_SIZE	10000

org.broadinstitute.hellbender.engine.VariantShard

Modifier and Type	Constant Field	Value
public static final int	VARIANT_SHARDSIZE	1000

org.broadinstitute.hellbender.engine.VariantWalkerBase

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_DRIVING_VARIANTS_LOOKAHEAD_BASES	100000

org.broadinstitute.hellbender.engine.filters.MateDistantReadFilter

Modifier and Type	Constant Field	Value
public static final int	mateTooDistantLength	1000

org.broadinstitute.hellbender.engine.filters.ReadGroupBlackListReadFilter

Modifier and Type	Constant Field	Value
public static final java.lang.String	FILTER_ENTRY_SEPARATOR	":"

org.broadinstitute.hellbender.engine.filters.VariantFilter

Modifier and Type	Constant Field	Value
public static final long	serialVersionUID	1L

org.broadinstitute.hellbender.engine.spark.AssemblyRegionArgumentCollection

Modifier and Type	Constant Field	Value
public static final java.lang.String	ASSEMBLY_PADDING_LONG_NAME	"assembly-region-padding"
public static final java.lang.String	ASSEMBLY_REGION_OUT_LONG_NAME	"assembly-region-out"
public static final double	DEFAULT_ACTIVE_PROB_THRESHOLD	0.002
public static final int	DEFAULT_ASSEMBLY_REGION_PADDING	100
public static final int	DEFAULT_MAX_ASSEMBLY_REGION_SIZE	300
public static final int	DEFAULT_MAX_PROB_PROPAGATION_DISTANCE	50
public static final int	DEFAULT_MAX_READS_PER_ALIGNMENT	50
public static final int	DEFAULT_MIN_ASSEMBLY_REGION_SIZE	50
public static final java.lang.String	FORCE_ACTIVE_REGIONS_LONG_NAME	"force-active"
public static final java.lang.String	INDEL_PADDING_LONG_NAME	"padding-around-indels"
public static final java.lang.String	MAX_ASSEMBLY_LONG_NAME	"max-assembly-region-size"
public static final java.lang.String	MAX_STARTS_LONG_NAME	"max-reads-per-alignment-start"
public static final java.lang.String	MIN_ASSEMBLY_LONG_NAME	"min-assembly-region-size"
public static final java.lang.String	PROPAGATION_LONG_NAME	"max-prob-propagation-distance"
public static final java.lang.String	SNP_PADDING_LONG_NAME	"padding-around-snps"
public static final java.lang.String	STR_PADDING_LONG_NAME	"padding-around-strs"
public static final java.lang.String	THRESHOLD_LONG_NAME	"active-probability-threshold"

org.broadinstitute.hellbender.engine.spark.AssemblyRegionReadShardArgumentCollection

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_READSHARD_PADDING_SIZE	100
public static final int	DEFAULT_READSHARD_SIZE	5000

org.broadinstitute.hellbender.engine.spark.GATKSparkTool

Modifier and Type	Constant Field	Value
public static final java.lang.String	BAM_PARTITION_SIZE_LONG_NAME	"bam-partition-size"
public static final java.lang.String	CREATE_OUTPUT_BAM_SPLITTING_INDEX_LONG_NAME	"create-output-bam-splitting-index"
public static final java.lang.String	NUM_REDUCERS_LONG_NAME	"num-reducers"
public static final java.lang.String	OUTPUT_SHARD_DIR_LONG_NAME	"output-shard-tmp-dir"
public static final java.lang.String	SHARDED_OUTPUT_LONG_NAME	"sharded-output"
public static final java.lang.String	SPLITTING_INDEX_GRANULARITY	"splitting-index-granularity"
public static final java.lang.String	USE_NIO	"use-nio"

org.broadinstitute.hellbender.engine.spark.ReadWalkerSpark

Modifier and Type	Constant Field	Value
public static final int	FEATURE_CACHE_LOOKAHEAD	1000

org.broadinstitute.hellbender.engine.spark.SparkCommandLineArgumentCollection

Modifier and Type	Constant Field	Value
public static final java.lang.String	SPARK_MASTER_LONG_NAME	"spark-master"
public static final java.lang.String	SPARK_VERBOSITY_LONG_NAME	"spark-verbosity"

org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram

Modifier and Type	Constant Field	Value
public static final java.lang.String	SPARK_PROGRAM_NAME_LONG_NAME	"program-name"

org.broadinstitute.hellbender.engine.spark.VariantWalkerSpark

Modifier and Type	Constant Field	Value
public static final int	FEATURE_CACHE_LOOKAHEAD	100000

org.broadinstitute.hellbender.engine.spark.datasources.ReferenceTwoBitSparkSource

Modifier and Type	Constant Field	Value
public static final java.lang.String	TWO_BIT_EXTENSION	".2bit"

org.broadinstitute.hellbender.metrics.MultiLevelCollector<METRIC_TYPE extends htsjdk.samtools.metrics.MetricBase,HISTOGRAM_KEY extends java.lang.Comparable<HISTOGRAM_KEY>,ARGTYPE>

Modifier and Type	Constant Field	Value
public static final java.lang.String	UNKNOWN	"unknown"

org.broadinstitute.hellbender.metrics.QualityYieldMetricsArgumentCollection

Modifier and Type	Constant Field	Value
public static final long	serialVersionUID	1L

org.broadinstitute.hellbender.tools.AddOriginalAlignmentTags

Modifier and Type	Constant Field	Value
public static final java.lang.String	MATE_CONTIG_TAG_NAME	"XM"
public static final java.lang.String	OA_SEPARATOR	","
public static final java.lang.String	OA_TAG_NAME	"OA"

org.broadinstitute.hellbender.tools.ClipReads

Modifier and Type	Constant Field	Value
public static final java.lang.String	CLIP_REPRESENTATION_LONG_NAME	"clip-representation"
public static final java.lang.String	CLIP_REPRESENTATION_SHORT_NAME	"CR"
public static final java.lang.String	CLIP_SEQUENCE_LONG_NAME	"clip-sequence"
public static final java.lang.String	CLIP_SEQUENCE_SHORT_NAME	"X"
public static final java.lang.String	CLIP_SEQUENCES_FILE_LONG_NAME	"clip-sequences-file"
public static final java.lang.String	CLIP_SEQUENCES_FILE_SHORT_NAME	"XF"
public static final java.lang.String	CYCLES_TO_TRIM_LONG_NAME	"cycles-to-trim"
public static final java.lang.String	CYCLES_TO_TRIM_SHORT_NAME	"CT"
public static final java.lang.String	OUTPUT_STATISTICS_LONG_NAME	"output-statistics"
public static final java.lang.String	OUTPUT_STATISTICS_SHORT_NAME	"os"
public static final java.lang.String	Q_TRIMMING_THRESHOLD_LONG_NAME	"q-trimming-threshold"
public static final java.lang.String	Q_TRIMMING_THRESHOLD_SHORT_NAME	"QT"
public static final java.lang.String	READ_LONG_NAME	"read"
public static final java.lang.String	READ_SHORT_NAME	"read"

org.broadinstitute.hellbender.tools.ConvertHeaderlessHadoopBamShardToBam

Modifier and Type	Constant Field	Value
public static final java.lang.String	BAM_SHARD_LONG_NAME	"bam-shard"
public static final java.lang.String	BAM_WITH_HEADER_LONG_NAME	"bam-with-header"
public static final java.lang.String	OUTPUT_LONG_NAME	"output"
public static final java.lang.String	OUTPUT_SHORT_NAME	"O"

org.broadinstitute.hellbender.tools.GatherVcfsCloud

Modifier and Type	Constant Field	Value
public static final java.lang.String	GATHER_TYPE_LONG_NAME	"gather-type"
public static final java.lang.String	IGNORE_SAFETY_CHECKS_LONG_NAME	"ignore-safety-checks"

org.broadinstitute.hellbender.tools.GetSampleName

Modifier and Type	Constant Field	Value
public static final java.lang.String	STANDARD_ENCODING	"UTF-8"
public static final java.lang.String	URL_ENCODING_LONG_NAME	"use-url-encoding"
public static final java.lang.String	URL_ENCODING_SHORT_NAME	"encode"

org.broadinstitute.hellbender.tools.HaplotypeCallerSpark

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_READSHARD_SIZE	5000

org.broadinstitute.hellbender.tools.HtsgetReader

Modifier and Type	Constant Field	Value
public static final java.lang.String	CHECK_MD5_LONG_NAME	"check-md5"
public static final java.lang.String	CLASS_LONG_NAME	"class"
public static final java.lang.String	FIELDS_LONG_NAME	"field"
public static final java.lang.String	FORMAT_LONG_NAME	"format"
public static final java.lang.String	ID_LONG_NAME	"id"
public static final java.lang.String	NOTAGS_LONG_NAME	"notag"
public static final java.lang.String	NUM_THREADS_LONG_NAME	"reader-threads"
public static final java.lang.String	TAGS_LONG_NAME	"tag"
public static final java.lang.String	URL_LONG_NAME	"url"

org.broadinstitute.hellbender.tools.IndexFeatureFile

Modifier and Type	Constant Field	Value
public static final java.lang.String	GVCF_FILE_EXTENSION	".g.vcf"
public static final int	OPTIMAL_GVCF_INDEX_BIN_SIZE	128000

org.broadinstitute.hellbender.tools.LocalAssembler

Modifier and Type	Constant Field	Value
public static final int	MIN_GAPFILL_COUNT_DEFAULT	3
public static final int	MIN_SV_SIZE_DEFAULT	50
public static final int	MIN_THIN_OBS_DEFAULT	4
public static final byte	QMIN_DEFAULT	25
public static final int	TOO_MANY_SCAFFOLDS_DEFAULT	50000
public static final int	TOO_MANY_TRAVERSALS_DEFAULT	100000

org.broadinstitute.hellbender.tools.LocalAssembler.Kmer

Modifier and Type	Constant Field	Value
public static final long	KMASK	4611686018427387903L
public static final int	KSIZE	31

org.broadinstitute.hellbender.tools.SplitReads

Modifier and Type	Constant Field	Value
public static final java.lang.String	LIBRARY_NAME_LONG_NAME	"split-library-name"
public static final java.lang.String	LIBRARY_NAME_SHORT_NAME	"LB"
public static final java.lang.String	READ_GROUP_LONG_NAME	"split-read-group"
public static final java.lang.String	READ_GROUP_SHORT_NAME	"RG"
public static final java.lang.String	SAMPLE_LONG_NAME	"split-sample"
public static final java.lang.String	SAMPLE_SHORT_NAME	"SM"
public static final java.lang.String	UNKNOWN_OUT_PREFIX	"unknown"

org.broadinstitute.hellbender.tools.copynumber.AnnotateIntervals

Modifier and Type	Constant Field	Value
public static final java.lang.String	FEATURE_QUERY_LOOKAHEAD	"feature-query-lookahead"
public static final java.lang.String	MAPPABILITY_TRACK_PATH_LONG_NAME	"mappability-track"
public static final java.lang.String	SEGMENTAL_DUPLICATION_TRACK_PATH_LONG_NAME	"segmental-duplication-track"

org.broadinstitute.hellbender.tools.copynumber.CallCopyRatioSegments

Modifier and Type	Constant Field	Value
public static final java.lang.String	CALLING_COPY_RATIO_Z_SCORE_THRESHOLD_LONG_NAME	"calling-copy-ratio-z-score-threshold"
public static final java.lang.String	LEGACY_SEGMENTS_FILE_SUFFIX	".igv.seg"
public static final java.lang.String	NEUTRAL_SEGMENT_COPY_RATIO_LOWER_BOUND_LONG_NAME	"neutral-segment-copy-ratio-lower-bound"
public static final java.lang.String	NEUTRAL_SEGMENT_COPY_RATIO_UPPER_BOUND_LONG_NAME	"neutral-segment-copy-ratio-upper-bound"
public static final java.lang.String	OUTLIER_NEUTRAL_SEGMENT_COPY_RATIO_Z_SCORE_THRESHOLD_LONG_NAME	"outlier-neutral-segment-copy-ratio-z-score-threshold"

org.broadinstitute.hellbender.tools.copynumber.CollectAllelicCounts

Modifier and Type	Constant Field	Value
public static final java.lang.String	MINIMUM_BASE_QUALITY_LONG_NAME	"minimum-base-quality"

org.broadinstitute.hellbender.tools.copynumber.CollectReadCounts

Modifier and Type	Constant Field	Value
public static final java.lang.String	FORMAT_LONG_NAME	"format"

org.broadinstitute.hellbender.tools.copynumber.CreateReadCountPanelOfNormals

Modifier and Type	Constant Field	Value
public static final java.lang.String	EXTREME_OUTLIER_TRUNCATION_PERCENTILE_LONG_NAME	"extreme-outlier-truncation-percentile"
public static final java.lang.String	EXTREME_SAMPLE_MEDIAN_PERCENTILE_LONG_NAME	"extreme-sample-median-percentile"
public static final java.lang.String	IMPUTE_ZEROS_LONG_NAME	"do-impute-zeros"
public static final java.lang.String	MAXIMUM_CHUNK_SIZE	"maximum-chunk-size"
public static final java.lang.String	MAXIMUM_ZEROS_IN_INTERVAL_PERCENTAGE_LONG_NAME	"maximum-zeros-in-interval-percentage"
public static final java.lang.String	MAXIMUM_ZEROS_IN_SAMPLE_PERCENTAGE_LONG_NAME	"maximum-zeros-in-sample-percentage"
public static final java.lang.String	MINIMUM_INTERVAL_MEDIAN_PERCENTILE_LONG_NAME	"minimum-interval-median-percentile"

org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy

Modifier and Type	Constant Field	Value
public static final java.lang.String	CALLS_PATH_SUFFIX	"-calls"
public static final java.lang.String	CASE_DETERMINE_PLOIDY_AND_DEPTH_PYTHON_SCRIPT	"case_determine_ploidy_and_depth.py"
public static final java.lang.String	COHORT_DETERMINE_PLOIDY_AND_DEPTH_PYTHON_SCRIPT	"cohort_determine_ploidy_and_depth.py"
public static final java.lang.String	CONTIG_PLOIDY_PRIORS_FILE_LONG_NAME	"contig-ploidy-priors"
public static final java.lang.String	INPUT_MODEL_INTERVAL_FILE	"interval_list.tsv"
public static final java.lang.String	MODEL_PATH_SUFFIX	"-model"

org.broadinstitute.hellbender.tools.copynumber.FilterIntervals

Modifier and Type	Constant Field	Value
public static final java.lang.String	EXTREME_COUNT_FILTER_MAXIMUM_PERCENTILE_LONG_NAME	"extreme-count-filter-maximum-percentile"
public static final java.lang.String	EXTREME_COUNT_FILTER_MINIMUM_PERCENTILE_LONG_NAME	"extreme-count-filter-minimum-percentile"
public static final java.lang.String	EXTREME_COUNT_FILTER_PERCENTAGE_OF_SAMPLES_LONG_NAME	"extreme-count-filter-percentage-of-samples"
public static final java.lang.String	LOW_COUNT_FILTER_COUNT_THRESHOLD_LONG_NAME	"low-count-filter-count-threshold"
public static final java.lang.String	LOW_COUNT_FILTER_PERCENTAGE_OF_SAMPLES_LONG_NAME	"low-count-filter-percentage-of-samples"
public static final java.lang.String	MAXIMUM_GC_CONTENT_LONG_NAME	"maximum-gc-content"
public static final java.lang.String	MAXIMUM_MAPPABILITY_LONG_NAME	"maximum-mappability"
public static final java.lang.String	MAXIMUM_SEGMENTAL_DUPLICATION_CONTENT_LONG_NAME	"maximum-segmental-duplication-content"
public static final java.lang.String	MINIMUM_GC_CONTENT_LONG_NAME	"minimum-gc-content"
public static final java.lang.String	MINIMUM_MAPPABILITY_LONG_NAME	"minimum-mappability"
public static final java.lang.String	MINIMUM_SEGMENTAL_DUPLICATION_CONTENT_LONG_NAME	"minimum-segmental-duplication-content"

org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller

Modifier and Type	Constant Field	Value
public static final java.lang.String	CALLS_PATH_SUFFIX	"-calls"
public static final java.lang.String	CASE_SAMPLE_CALLING_PYTHON_SCRIPT	"case_denoising_calling.py"
public static final java.lang.String	COHORT_DENOISING_CALLING_PYTHON_SCRIPT	"cohort_denoising_calling.py"
public static final java.lang.String	CONTIG_PLOIDY_CALLS_DIRECTORY_LONG_NAME	"contig-ploidy-calls"
public static final java.lang.String	INPUT_MODEL_INTERVAL_FILE	"interval_list.tsv"
public static final java.lang.String	MODEL_PATH_SUFFIX	"-model"
public static final java.lang.String	RUN_MODE_LONG_NAME	"run-mode"
public static final java.lang.String	TRACKING_PATH_SUFFIX	"-tracking"

org.broadinstitute.hellbender.tools.copynumber.ModelSegments

Modifier and Type	Constant Field	Value
public static final java.lang.String	ALLELE_FRACTION_LEGACY_SEGMENTS_FILE_SUFFIX	".af.igv.seg"
public static final java.lang.String	ALLELE_FRACTION_MODEL_PARAMETER_FILE_SUFFIX	".af.param"
public static final java.lang.String	BEGIN_FIT_FILE_TAG	".modelBegin"
public static final java.lang.String	COPY_RATIO_LEGACY_SEGMENTS_FILE_SUFFIX	".cr.igv.seg"
public static final java.lang.String	COPY_RATIO_MODEL_PARAMETER_FILE_SUFFIX	".cr.param"
public static final java.lang.String	COPY_RATIO_SEGMENTS_FOR_CALLER_FILE_SUFFIX	".cr.seg"
public static final java.lang.String	FINAL_FIT_FILE_TAG	".modelFinal"
public static final java.lang.String	HET_ALLELIC_COUNTS_FILE_SUFFIX	".hets.tsv"
public static final java.lang.String	NORMAL_HET_ALLELIC_COUNTS_FILE_SUFFIX	".hets.normal.tsv"
public static final java.lang.String	PICARD_INTERVAL_LIST_FILE_SUFFIX	".interval_list"
public static final java.lang.String	SEGMENTS_FILE_SUFFIX	".seg"

org.broadinstitute.hellbender.tools.copynumber.PostprocessGermlineCNVCalls

Modifier and Type	Constant Field	Value
public static final java.lang.String	ALLOSOMAL_CONTIG_LONG_NAME	"allosomal-contig"
public static final java.lang.String	AUTOSOMAL_REF_COPY_NUMBER_LONG_NAME	"autosomal-ref-copy-number"
public static final java.lang.String	CALLS_SHARD_PATH_LONG_NAME	"calls-shard-path"
public static final java.lang.String	CLUSTERED_FILE_LONG_NAME	"clustered-breakpoints"
public static final java.lang.String	CONTIG_PLOIDY_CALLS_LONG_NAME	"contig-ploidy-calls"
public static final java.lang.String	DUPLICATION_QS_THRESHOLD_LONG_NAME	"duplication-qs-threshold"
public static final java.lang.String	HET_DEL_QS_THRESHOLD_LONG_NAME	"het-deletion-qs-threshold"
public static final java.lang.String	HOM_DEL_QS_THRESHOLD_LONG_NAME	"hom-deletion-qs-threshold"
public static final java.lang.String	INPUT_INTERVALS_LONG_NAME	"input-intervals-vcf"
public static final java.lang.String	MODEL_SHARD_PATH_LONG_NAME	"model-shard-path"
public static final java.lang.String	OUTPUT_DENOISED_COPY_RATIOS_LONG_NAME	"output-denoised-copy-ratios"
public static final java.lang.String	OUTPUT_INTERVALS_VCF_LONG_NAME	"output-genotyped-intervals"
public static final java.lang.String	OUTPUT_SEGMENTS_VCF_LONG_NAME	"output-genotyped-segments"
public static final java.lang.String	SAMPLE_INDEX_LONG_NAME	"sample-index"
public static final java.lang.String	SEGMENT_GERMLINE_CNV_CALLS_PYTHON_SCRIPT	"segment_gcnv_calls.py"
public static final java.lang.String	SITE_FREQUENCY_THRESHOLD_LONG_NAME	"site-frequency-threshold"

org.broadinstitute.hellbender.tools.copynumber.PreprocessIntervals

Modifier and Type	Constant Field	Value
public static final java.lang.String	BIN_LENGTH_LONG_NAME	"bin-length"
public static final java.lang.String	PADDING_LONG_NAME	"padding"

org.broadinstitute.hellbender.tools.copynumber.arguments.CopyNumberStandardArgument

Modifier and Type	Constant Field	Value
public static final java.lang.String	ALLELIC_COUNTS_FILE_LONG_NAME	"allelic-counts"
public static final java.lang.String	ANNOTATED_INTERVALS_FILE_LONG_NAME	"annotated-intervals"
public static final java.lang.String	COUNT_PANEL_OF_NORMALS_FILE_LONG_NAME	"count-panel-of-normals"
public static final java.lang.String	DENOISED_COPY_RATIOS_FILE_LONG_NAME	"denoised-copy-ratios"
public static final java.lang.String	MODEL_LONG_NAME	"model"
public static final java.lang.String	NORMAL_ALLELIC_COUNTS_FILE_LONG_NAME	"normal-allelic-counts"
public static final java.lang.String	NUMBER_OF_EIGENSAMPLES_LONG_NAME	"number-of-eigensamples"
public static final java.lang.String	OUTPUT_PREFIX_LONG_NAME	"output-prefix"
public static final java.lang.String	SEGMENTS_FILE_LONG_NAME	"segments"
public static final java.lang.String	STANDARDIZED_COPY_RATIOS_FILE_LONG_NAME	"standardized-copy-ratios"

org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineCallingArgumentCollection

Modifier and Type	Constant Field	Value
public static final java.lang.String	CLASS_COHERENCE_LENGTH_LONG_NAME	"class-coherence-length"
public static final java.lang.String	CNV_COHERENCE_LENGTH_LONG_NAME	"cnv-coherence-length"
public static final java.lang.String	MAX_COPY_NUMBER_LONG_NAME	"max-copy-number"
public static final java.lang.String	P_ACTIVE_LONG_NAME	"p-active"
public static final java.lang.String	P_ALT_LONG_NAME	"p-alt"

org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineContigPloidyModelArgumentCollection

Modifier and Type	Constant Field	Value
public static final java.lang.String	GLOBAL_PSI_SCALE_LONG_NAME	"global-psi-scale"
public static final java.lang.String	MAPPING_ERROR_RATE_LONG_NAME	"mapping-error-rate"
public static final java.lang.String	MEAN_BIAS_STANDARD_DEVIATION_LONG_NAME	"mean-bias-standard-deviation"
public static final java.lang.String	SAMPLE_PSI_SCALE_LONG_NAME	"sample-psi-scale"

org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineDenoisingModelArgumentCollection

Modifier and Type	Constant Field	Value
public static final java.lang.String	ACTIVE_CLASS_PADDING_HYBRID_MODE_LONG_NAME	"active-class-padding-hybrid-mode"
public static final java.lang.String	COPY_NUMBER_POSTERIOR_EXPECTATION_MODE_LONG_NAME	"copy-number-posterior-expectation-mode"
public static final java.lang.String	DEPTH_CORRECTION_TAU_LONG_NAME	"depth-correction-tau"
public static final java.lang.String	ENABLE_BIAS_FACTORS_LONG_NAME	"enable-bias-factors"
public static final java.lang.String	GC_CURVE_STANDARD_DEVIATION_LONG_NAME	"gc-curve-standard-deviation"
public static final java.lang.String	INIT_ARD_REL_UNEXPLAINED_VARIANCE_LONG_NAME	"init-ard-rel-unexplained-variance"
public static final java.lang.String	INTERVAL_PSI_SCALE_LONG_NAME	"interval-psi-scale"
public static final java.lang.String	LOG_MEAN_BIAS_STANDARD_DEVIATION_LONG_NAME	"log-mean-bias-standard-deviation"
public static final java.lang.String	MAPPING_ERROR_RATE_LONG_NAME	"mapping-error-rate"
public static final java.lang.String	MAX_BIAS_FACTORS_LONG_NAME	"max-bias-factors"
public static final java.lang.String	NUM_GC_BINS_LONG_NAME	"num-gc-bins"
public static final java.lang.String	NUM_SAMPLES_CR_APPROX_LONG_NAME	"num-samples-copy-ratio-approx"
public static final java.lang.String	SAMPLE_PSI_SCALE_LONG_NAME	"sample-psi-scale"

org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection

Modifier and Type	Constant Field	Value
public static final java.lang.String	ADAMAX_BETA_1_LONG_NAME	"adamax-beta-1"
public static final java.lang.String	ADAMAX_BETA_2_LONG_NAME	"adamax-beta-2"
public static final java.lang.String	CALLER_EXTERNAL_ADMIXING_RATE_LONG_NAME	"caller-external-admixing-rate"
public static final java.lang.String	CALLER_INTERNAL_ADMIXING_RATE_LONG_NAME	"caller-internal-admixing-rate"
public static final java.lang.String	CALLER_UPDATE_CONVERGENCE_THRESHOLD_LONG_NAME	"caller-update-convergence-threshold"
public static final java.lang.String	CONVERGENCE_SNR_AVERAGING_WINDOW_LONG_NAME	"convergence-snr-averaging-window"
public static final java.lang.String	CONVERGENCE_SNR_COUNTDOWN_WINDOW_LONG_NAME	"convergence-snr-countdown-window"
public static final java.lang.String	CONVERGENCE_SNR_TRIGGER_THRESHOLD_LONG_NAME	"convergence-snr-trigger-threshold"
public static final java.lang.String	DISABLE_ANNEALING_RATE_LONG_NAME	"disable-annealing"
public static final java.lang.String	DISABLE_CALLER_LONG_NAME	"disable-caller"
public static final java.lang.String	DISABLE_SAMPLER_LONG_NAME	"disable-sampler"
public static final java.lang.String	INITIAL_TEMPERATURE_LONG_NAME	"initial-temperature"
public static final java.lang.String	LEARNING_RATE_LONG_NAME	"learning-rate"
public static final java.lang.String	LOG_EMISSION_SAMPLES_PER_ROUND_LONG_NAME	"log-emission-samples-per-round"
public static final java.lang.String	LOG_EMISSION_SAMPLING_MEDIAN_REL_ERROR_LONG_NAME	"log-emission-sampling-median-rel-error"
public static final java.lang.String	LOG_EMISSION_SAMPLING_ROUNDS_LONG_NAME	"log-emission-sampling-rounds"
public static final java.lang.String	MAX_ADVI_ITER_FIRST_EPOCH_LONG_NAME	"max-advi-iter-first-epoch"
public static final java.lang.String	MAX_ADVI_ITER_SUBSEQUENT_EPOCHS_LONG_NAME	"max-advi-iter-subsequent-epochs"
public static final java.lang.String	MAX_CALLING_ITERS_LONG_NAME	"max-calling-iters"
public static final java.lang.String	MAX_TRAINING_EPOCHS_LONG_NAME	"max-training-epochs"
public static final java.lang.String	MIN_TRAINING_EPOCHS_LONG_NAME	"min-training-epochs"
public static final java.lang.String	NUM_THERMAL_ADVI_ITERS_LONG_NAME	"num-thermal-advi-iters"

org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticGenotypingArgumentCollection

Modifier and Type	Constant Field	Value
public static final java.lang.String	GENOTYPING_BASE_ERROR_RATE_LONG_NAME	"genotyping-base-error-rate"
public static final java.lang.String	GENOTYPING_HOMOZYGOUS_LOG_RATIO_THRESHOLD_LONG_NAME	"genotyping-homozygous-log-ratio-threshold"
public static final java.lang.String	MINIMUM_TOTAL_ALLELE_COUNT_CASE_LONG_NAME	"minimum-total-allele-count-case"
public static final java.lang.String	MINIMUM_TOTAL_ALLELE_COUNT_NORMAL_LONG_NAME	"minimum-total-allele-count-normal"
public static final long	serialVersionUID	1L

org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticModelingArgumentCollection

Modifier and Type	Constant Field	Value
public static final java.lang.String	MAXIMUM_NUMBER_OF_SMOOTHING_ITERATIONS_LONG_NAME	"maximum-number-of-smoothing-iterations"
public static final java.lang.String	MINOR_ALLELE_FRACTION_PRIOR_ALPHA_LONG_NAME	"minor-allele-fraction-prior-alpha"
public static final java.lang.String	NUMBER_OF_BURN_IN_SAMPLES_ALLELE_FRACTION_LONG_NAME	"number-of-burn-in-samples-allele-fraction"
public static final java.lang.String	NUMBER_OF_BURN_IN_SAMPLES_COPY_RATIO_LONG_NAME	"number-of-burn-in-samples-copy-ratio"
public static final java.lang.String	NUMBER_OF_SAMPLES_ALLELE_FRACTION_LONG_NAME	"number-of-samples-allele-fraction"
public static final java.lang.String	NUMBER_OF_SAMPLES_COPY_RATIO_LONG_NAME	"number-of-samples-copy-ratio"
public static final java.lang.String	NUMBER_OF_SMOOTHING_ITERATIONS_PER_FIT_LONG_NAME	"number-of-smoothing-iterations-per-fit"
public static final long	serialVersionUID	1L
public static final java.lang.String	SMOOTHING_CREDIBLE_INTERVAL_THRESHOLD_ALLELE_FRACTION_LONG_NAME	"smoothing-credible-interval-threshold-allele-fraction"
public static final java.lang.String	SMOOTHING_CREDIBLE_INTERVAL_THRESHOLD_COPY_RATIO_LONG_NAME	"smoothing-credible-interval-threshold-copy-ratio"

org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticSegmentationArgumentCollection

Modifier and Type	Constant Field	Value
public static final java.lang.String	KERNEL_APPROXIMATION_DIMENSION_LONG_NAME	"kernel-approximation-dimension"
public static final java.lang.String	KERNEL_SCALING_ALLELE_FRACTION_LONG_NAME	"kernel-scaling-allele-fraction"
public static final java.lang.String	KERNEL_VARIANCE_ALLELE_FRACTION_LONG_NAME	"kernel-variance-allele-fraction"
public static final java.lang.String	KERNEL_VARIANCE_COPY_RATIO_LONG_NAME	"kernel-variance-copy-ratio"
public static final java.lang.String	MAXIMUM_NUMBER_OF_SEGMENTS_PER_CHROMOSOME_LONG_NAME	"maximum-number-of-segments-per-chromosome"
public static final java.lang.String	NUMBER_OF_CHANGEPOINTS_PENALTY_FACTOR_LONG_NAME	"number-of-changepoints-penalty-factor"
public static final long	serialVersionUID	1L
public static final java.lang.String	WINDOW_SIZE_LONG_NAME	"window-size"

org.broadinstitute.hellbender.tools.copynumber.formats.CopyNumberFormatsUtils

Modifier and Type	Constant Field	Value
public static final java.lang.String	COMMENT_PREFIX	"@"
public static final java.lang.String	DOUBLE_FORMAT	"%.6f"

org.broadinstitute.hellbender.tools.copynumber.gcnv.GermlineCNVNamingConstants

Modifier and Type	Constant Field	Value
public static final java.lang.String	BASELINE_COPY_NUMBER_FILE_NAME	"baseline_copy_number_t.tsv"
public static final java.lang.String	BASELINE_COPY_NUMBER_TABLE_COLUMN	"BASELINE_COPY_NUMBER"
public static final java.lang.String	COPY_NUMBER_POSTERIOR_FILE_NAME	"log_q_c_tc.tsv"
public static final java.lang.String	COPY_NUMBER_SEGMENTS_FILE_NAME	"copy_number_segments.tsv"
public static final java.lang.String	COPY_NUMBER_TABLE_COLUMN_PREFIX	"COPY_NUMBER_"
public static final java.lang.String	DEFAULT_GCNV_OUTPUT_COLUMN_PREFIX	"VALUE_"
public static final java.lang.String	DENOISED_COPY_RATIO_MEAN_FILE_NAME	"mu_denoised_copy_ratio_t.tsv"
public static final java.lang.String	INTERVAL_LIST_FILE_NAME	"interval_list.tsv"
public static final java.lang.String	SAMPLE_NAME_TXT_FILE	"sample_name.txt"
public static final java.lang.String	SAMPLE_PREFIX	"SAMPLE_"

org.broadinstitute.hellbender.tools.copynumber.gcnv.GermlineCNVSegmentVariantComposer

Modifier and Type	Constant Field	Value
public static final java.lang.String	CURRENT_SCHEMA_VERSION	"2.0"
public static final java.lang.String	NP	"NP"
public static final java.lang.String	QA	"QA"
public static final java.lang.String	QS	"QS"
public static final java.lang.String	QSE	"QSE"
public static final java.lang.String	QSS	"QSS"
public static final java.lang.String	SCHEMA_HEADER_KEY	"gcnvVcfSchemaVersion"

org.broadinstitute.hellbender.tools.copynumber.utils.CombineSegmentBreakpoints

Modifier and Type	Constant Field	Value
public static final java.lang.String	COLUMNS_OF_INTEREST_LONG_NAME	"columns-of-interest"
public static final java.lang.String	LABELS_LONG_NAME	"labels"

org.broadinstitute.hellbender.tools.copynumber.utils.HDF5Utils

Modifier and Type	Constant Field	Value
public static final java.lang.String	CHUNK_INDEX_PATH_SUFFIX	"/chunk_"
public static final java.lang.String	INTERVAL_CONTIG_NAMES_SUB_PATH	"/indexed_contig_names"
public static final java.lang.String	INTERVAL_MATRIX_SUB_PATH	"/transposed_index_start_end"
public static final int	MAX_NUMBER_OF_VALUES_PER_HDF5_MATRIX	268435455
public static final java.lang.String	NUMBER_OF_CHUNKS_SUB_PATH	"/num_chunks"
public static final java.lang.String	NUMBER_OF_COLUMNS_SUB_PATH	"/num_columns"
public static final java.lang.String	NUMBER_OF_ROWS_SUB_PATH	"/num_rows"

org.broadinstitute.hellbender.tools.copynumber.utils.MergeAnnotatedRegionsByAnnotation

Modifier and Type	Constant Field	Value
public static final java.lang.String	ANNOTATIONS_TO_MATCH	"annotations-to-match"
public static final java.lang.String	MAX_MERGE_DISTANCE	"max-merge-distance"

org.broadinstitute.hellbender.tools.copynumber.utils.TagGermlineEvents

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_GERMLINE_TAG_PADDING_IN_BP	1000
public static final java.lang.String	GERMLINE_TAG_HEADER	"POSSIBLE_GERMLINE"
public static final java.lang.String	INPUT_CALL_HEADER	"input-call-header"
public static final java.lang.String	MATCHED_NORMAL_SEGMENT_FILE_LONG_NAME	"called-matched-normal-seg-file"
public static final java.lang.String	PADDING_IN_BP_LONG_NAME	"endpoint-padding"

org.broadinstitute.hellbender.tools.dragstr.CalibrateDragstrModel

Modifier and Type	Constant Field	Value
public static final java.lang.String	DEBUG_SITES_OUTPUT_FULL_NAME	"debug-sites-output"
public static final int	DEFAULT_DOWN_SAMPLE_SIZE	4096
public static final int	DEFAULT_SHARD_SIZE	1000000
public static final java.lang.String	DOWN_SAMPLE_SIZE_FULL_NAME	"down-sample-size"
public static final java.lang.String	FORCE_ESTIMATION_FULL_NAME	"force-estimation"
public static final int	MINIMUM_DOWN_SAMPLE_SIZE	512
public static final int	MINIMUM_SHARD_SIZE	100
public static final java.lang.String	PARALLEL_FULL_NAME	"parallel"
public static final java.lang.String	SHARD_SIZE_FULL_NAME	"shard-size"
public static final java.lang.String	STR_TABLE_PATH_FULL_NAME	"str-table-path"
public static final java.lang.String	STR_TABLE_PATH_SHORT_NAME	"str"
public static final int	SYSTEM_SUGGESTED_THREAD_NUMBER	0
public static final java.lang.String	THREADS_FULL_NAME	"threads"

org.broadinstitute.hellbender.tools.dragstr.ComposeSTRTableFile

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_REFERENCE_SEQUENCE_BUFFER_SIZE	100000
public static final java.lang.String	GENERATE_SITES_TEXT_OUTPUT_FULL_NAME	"generate-sites-text-output"
public static final int	MAXIMUM_REFERENCE_SEQUENCE_BUFFER_SIZE	100000000
public static final int	MINIMUM_REFERENCE_SEQUENCE_BUFFER_SIZE	1024
public static final java.lang.String	REFERENCE_SEQUENCE_BUFFER_SIZE_FULL_NAME	"reference-sequence-buffer-size"

org.broadinstitute.hellbender.tools.dragstr.DragstrHyperParameters

Modifier and Type	Constant Field	Value
public static final java.lang.String	API_MONO_THRESHOLD_FULL_NAME	"api-mono-threshold"
public static final java.lang.String	API_VALUES_ARGUMENT_FULL_NAME	"api-values"
public static final int	DEFAULT_API_MONO_THRESHOLD	3
public static final double	DEFAULT_HET_TO_HOM_RATIO	2.0
public static final int	DEFAULT_MAX_PERIOD	8
public static final int	DEFAULT_MAX_REPEAT_LENGTH	20
public static final int	DEFAULT_MIN_DEPTH	10
public static final int	DEFAULT_MIN_LOCI_COUNT	50
public static final int	DEFAULT_SAMPLING_MIN_MQ	20
public static final int	DEFAULT_SAMPLING_PADDING	5
public static final java.lang.String	GOP_VALUES_ARGUMENT_FULL_NAME	"gop-values"
public static final java.lang.String	GP_VALUES_ARGUMENT_FULL_NAME	"gp-values"
public static final java.lang.String	HET_TO_HOM_RATIO_FULL_NAME	"het-to-hom-ratio"
public static final java.lang.String	MAX_PERIOD_ARGUMENT_FULL_NAME	"max-period"
public static final java.lang.String	MAX_REPEATS_ARGUMENT_FULL_NAME	"max-repeats"
public static final java.lang.String	MIN_DEPTH_ARGUMENT_FULL_NAME	"minimum-depth"
public static final java.lang.String	MIN_DEPTH_ARGUMENT_SHORT_NAME	"md"
public static final java.lang.String	MIN_LOCI_COUNT_FULL_NAME	"min-loci-count"
public static final java.lang.String	SAMPLING_MIN_MQ_ARGUMENT_FULL_NAME	"sampling-min-mq"
public static final java.lang.String	SAMPLING_PADDING_ARGUMENT_FULL_NAME	"pileup-padding"

org.broadinstitute.hellbender.tools.dragstr.STRDecimationTable

Modifier and Type	Constant Field	Value
public static final java.lang.String	DEFAULT_DECIMATION_STR	"DEFAULT"
public static final java.lang.String	NO_DECIMATION_STR	"NONE"

org.broadinstitute.hellbender.tools.examples.ExampleTwoPassVariantWalker

Modifier and Type	Constant Field	Value
public static final java.lang.String	COPY_OF_QD_KEY_NAME	"QD_COPY"
public static final java.lang.String	QD_DISTANCE_FROM_MEAN	"QD_DIST"

org.broadinstitute.hellbender.tools.examples.metrics.multi.ExampleMultiMetricsArgumentCollection

Modifier and Type	Constant Field	Value
public static final long	serialVersionUID	1L

org.broadinstitute.hellbender.tools.examples.metrics.single.ExampleSingleMetricsArgumentCollection

Modifier and Type	Constant Field	Value
public static final long	serialVersionUID	1L

org.broadinstitute.hellbender.tools.funcotator.AminoAcid

Modifier and Type	Constant Field	Value
public static final int	CODON_LENGTH	3

org.broadinstitute.hellbender.tools.funcotator.BaseFuncotatorArgumentCollection

Modifier and Type	Constant Field	Value
protected static final java.lang.String	FuncotatorReferenceVersionB37	"b37"
public static final java.lang.String	FuncotatorReferenceVersionHg19	"hg19"
public static final java.lang.String	FuncotatorReferenceVersionHg38	"hg38"

org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory

Modifier and Type	Constant Field	Value
public static final java.lang.String	DEFAULT_VERSION_STRING	"UNKNOWN_VERSION"

org.broadinstitute.hellbender.tools.funcotator.FilterFuncotationsConstants

Modifier and Type	Constant Field	Value
public static final java.lang.String	CLINSIG_INFO_KEY	"CLINSIG"
public static final java.lang.String	CLINSIG_INFO_KEY_DESCRIPTION	"Rule(s) which caused this annotation to be flagged as clinically significant."
public static final java.lang.String	CLINSIG_INFO_NOT_SIGNIFICANT	"NONE"
public static final java.lang.String	FILTER_DELIMITER	","
public static final java.lang.String	NOT_CLINSIG_FILTER	"NOT_CLINSIG"
public static final java.lang.String	NOT_CLINSIG_FILTER_DESCRIPTION	"Filter for clinically insignificant variants."

org.broadinstitute.hellbender.tools.funcotator.FuncotationMap

Modifier and Type	Constant Field	Value
public static final java.lang.String	NO_TRANSCRIPT_AVAILABLE_KEY	"no_transcript"

org.broadinstitute.hellbender.tools.funcotator.FuncotatorArgumentDefinitions

Modifier and Type	Constant Field	Value
public static final java.lang.String	ALLELE_FREQUENCY_DATA_SOURCE_NAME	"allele-frequency-data-source"
public static final java.lang.String	ANNOTATION_DEFAULTS_LONG_NAME	"annotation-default"
public static final java.lang.String	ANNOTATION_OVERRIDES_LONG_NAME	"annotation-override"
public static final java.lang.String	DATA_SOURCES_PATH_LONG_NAME	"data-sources-path"
public static final java.lang.String	EXCLUSION_FIELDS_LONG_NAME	"exclude-field"
public static final int	FIVE_PRIME_FLANK_SIZE_DEFAULT_VALUE	5000
public static final java.lang.String	FIVE_PRIME_FLANK_SIZE_NAME	"five-prime-flank-size"
public static final java.lang.String	FORCE_B37_TO_HG19_REFERENCE_CONTIG_CONVERSION	"force-b37-to-hg19-reference-contig-conversion"
public static final int	LOOKAHEAD_CACHE_IN_BP_DEFAULT_VALUE	100000
public static final java.lang.String	LOOKAHEAD_CACHE_IN_BP_NAME	"lookahead-cache-bp"
public static final char	MAP_NAME_VALUE_DELIMITER	58
public static final java.lang.String	MIN_NUM_BASES_FOR_SEGMENT_FUNCOTATION	"min-num-bases-for-segment-funcotation"
public static final java.lang.String	OUTPUT_FORMAT_LONG_NAME	"output-file-format"
public static final java.lang.String	REANNOTATE_VCF_LONG_NAME	"reannotate-vcf"
public static final java.lang.String	REFERENCE_VERSION_LONG_NAME	"ref-version"
public static final java.lang.String	REMOVE_FILTERED_VARIANTS_LONG_NAME	"remove-filtered-variants"
public static final int	THREE_PRIME_FLANK_SIZE_DEFAULT_VALUE	0
public static final java.lang.String	THREE_PRIME_FLANK_SIZE_NAME	"three-prime-flank-size"
public static final java.lang.String	TRANSCRIPT_LIST_LONG_NAME	"transcript-list"
public static final java.lang.String	TRANSCRIPT_SELECTION_MODE_LONG_NAME	"transcript-selection-mode"

org.broadinstitute.hellbender.tools.funcotator.FuncotatorConstants

Modifier and Type	Constant Field	Value
public static final java.lang.String	B37_MITOCHONDRIAL_CONTIG_NAME	"MT"
public static final java.lang.String	DATASOURCE_NAME_FOR_INPUT_VCFS	"INPUT_VCF"
public static final java.lang.String	FUNCOTATOR_VERSION_VCF_HEADERLINE_KEY	"Funcotator Version"
public static final java.lang.String	HG19_MITOCHONDRIAL_CONTIG_NAME	"chrM"
public static final java.lang.String	HG38_MITOCHONDRIAL_CONTIG_NAME	"chrM"
public static final char	MASKED_ANY_BASE	78
public static final java.lang.String	UNKNOWN_VALUE_STRING	"__UNKNOWN__"

org.broadinstitute.hellbender.tools.funcotator.FuncotatorDataSourceDownloader

Modifier and Type	Constant Field	Value
public static final java.lang.String	EXTRACT_AFTER_DOWNLOAD	"extract-after-download"
public static final java.lang.String	GERMLINE_ARG_LONG_NAME	"germline"
public static final java.lang.String	OVERWRITE_ARG_LONG_NAME	"overwrite-output-file"
public static final java.lang.String	SOMATIC_ARG_LONG_NAME	"somatic"
public static final java.lang.String	VALIDATE_INTEGRITY_ARG_LONG_NAME	"validate-integrity"

org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_MIN_NUM_BASES_FOR_VALID_SEGMENT	150

org.broadinstitute.hellbender.tools.funcotator.StrandCorrectedAllele

Modifier and Type	Constant Field	Value
public static final long	serialVersionUID	1L

org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils

Modifier and Type	Constant Field	Value
public static final java.lang.String	CONFIG_FILE_FIELD_NAME_CONTIG_COLUMN	"contig_column"
public static final java.lang.String	CONFIG_FILE_FIELD_NAME_END_COLUMN	"end_column"
public static final java.lang.String	CONFIG_FILE_FIELD_NAME_GENCODE_FASTA_PATH	"gencode_fasta_path"
public static final java.lang.String	CONFIG_FILE_FIELD_NAME_IS_B37_DATA_SOURCE	"isB37DataSource"
public static final java.lang.String	CONFIG_FILE_FIELD_NAME_LOOKAHEAD_CACHE_BP	"lookAheadCacheBp"
public static final java.lang.String	CONFIG_FILE_FIELD_NAME_NAME	"name"
public static final java.lang.String	CONFIG_FILE_FIELD_NAME_NCBI_BUILD_VERSION	"ncbi_build_version"
public static final java.lang.String	CONFIG_FILE_FIELD_NAME_ORIGIN_LOCATION	"origin_location"
public static final java.lang.String	CONFIG_FILE_FIELD_NAME_PREPROCESSING_SCRIPT	"preprocessing_script"
public static final java.lang.String	CONFIG_FILE_FIELD_NAME_SRC_FILE	"src_file"
public static final java.lang.String	CONFIG_FILE_FIELD_NAME_START_COLUMN	"start_column"
public static final java.lang.String	CONFIG_FILE_FIELD_NAME_TYPE	"type"
public static final java.lang.String	CONFIG_FILE_FIELD_NAME_VERSION	"version"
public static final java.lang.String	CONFIG_FILE_FIELD_NAME_XSV_DELIMITER	"xsv_delimiter"
public static final java.lang.String	CONFIG_FILE_FIELD_NAME_XSV_KEY	"xsv_key"
public static final java.lang.String	CONFIG_FILE_FIELD_NAME_XSV_KEY_COLUMN	"xsv_key_column"
public static final java.lang.String	CONFIG_FILE_FIELD_NAME_XSV_PERMISSIVE_COLS	"xsv_permissive_cols"
public static final java.lang.String	DATA_SOURCES_BUCKET_PATH	"gs://broad-public-datasets/funcotator/"
public static final java.lang.String	DATA_SOURCES_FTP_PATH	"ftp://[email protected]/bundle/funcotator/"
public static final java.lang.String	DATA_SOURCES_NAME_PREFIX	"funcotator_dataSources"
public static final java.lang.String	DS_CHECKSUM_EXTENSION	".sha256"
public static final java.lang.String	DS_EXTENSION	".tar.gz"
public static final java.lang.String	DS_GERMLINE_NAME_MODIFIER	"g"
public static final java.lang.String	DS_SOMATIC_NAME_MODIFIER	"s"
public static final java.lang.String	MANIFEST_FILE_NAME	"MANIFEST.txt"

org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory

Modifier and Type	Constant Field	Value
public static final java.lang.String	DEFAULT_NAME	"Gencode"
public static final java.lang.String	END_EXON_SUFFIX	"_end_exon"
public static final java.lang.String	END_GENE_SUFFIX	"_end_gene"
public static final java.lang.String	GENES_SUFFIX	"_genes"
public static final java.lang.String	OTHER_TRANSCRIPTS_INFO_SEP	"_"
public static final java.lang.String	START_EXON_SUFFIX	"_start_exon"
public static final java.lang.String	START_GENE_SUFFIX	"_start_gene"

org.broadinstitute.hellbender.tools.funcotator.filtrationRules.AutosomalRecessiveConstants

Modifier and Type	Constant Field	Value
public static final java.lang.String	AR_INFO_VALUE	"AR"

org.broadinstitute.hellbender.tools.funcotator.filtrationRules.ClinVarFilter

Modifier and Type	Constant Field	Value
public static final java.lang.String	CLINSIG_INFO_VALUE	"CLINVAR"

org.broadinstitute.hellbender.tools.funcotator.filtrationRules.LmmFilter

Modifier and Type	Constant Field	Value
public static final java.lang.String	CLINSIG_INFO_VALUE	"LMM"

org.broadinstitute.hellbender.tools.funcotator.filtrationRules.LofFilter

Modifier and Type	Constant Field	Value
public static final java.lang.String	CLINSIG_INFO_VALUE	"LOF"

org.broadinstitute.hellbender.tools.funcotator.genelistoutput.GeneListOutputRenderer

Modifier and Type	Constant Field	Value
public static final java.lang.String	CONFIG_RESOURCE	"org/broadinstitute/hellbender/tools/funcotator/gene_list_output.config"

org.broadinstitute.hellbender.tools.funcotator.mafOutput.CustomMafFuncotationCreator

Modifier and Type	Constant Field	Value
public static final java.lang.String	BY_1KG	"by1000genomes"
public static final java.lang.String	BY_FREQ	"byFrequency"
public static final java.lang.String	MAF_DBSNP_VAL_STATUS_DELIMITER	";"
public static final java.lang.String	MAF_DBSNP_VAL_STATUS_FIELD	"custom_dbsnp_val_status"

org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants

Modifier and Type	Constant Field	Value
public static final java.lang.String	FieldName_Annotation_Transcript	"Annotation_Transcript"
public static final java.lang.String	FieldName_BAM_File	"BAM_File"
public static final java.lang.String	FieldName_CCLE_ONCOMAP_overlapping_mutations	"CCLE_ONCOMAP_overlapping_mutations"
public static final java.lang.String	FieldName_CCLE_ONCOMAP_total_mutations_in_gene	"CCLE_ONCOMAP_total_mutations_in_gene"
public static final java.lang.String	FieldName_cDNA_Change	"cDNA_Change"
public static final java.lang.String	FieldName_Center	"Center"
public static final java.lang.String	FieldName_CGC_Mutation_Type	"CGC_Mutation_Type"
public static final java.lang.String	FieldName_CGC_Other_Diseases	"CGC_Other_Diseases"
public static final java.lang.String	FieldName_CGC_Translocation_Partner	"CGC_Translocation_Partner"
public static final java.lang.String	FieldName_CGC_Tumor_Types_Germline	"CGC_Tumor_Types_Germline"
public static final java.lang.String	FieldName_CGC_Tumor_Types_Somatic	"CGC_Tumor_Types_Somatic"
public static final java.lang.String	FieldName_Chromosome	"Chromosome"
public static final java.lang.String	FieldName_Codon_Change	"Codon_Change"
public static final java.lang.String	FieldName_COSMIC_fusion_genes	"COSMIC_fusion_genes"
public static final java.lang.String	FieldName_COSMIC_overlapping_mutations	"COSMIC_overlapping_mutations"
public static final java.lang.String	FieldName_COSMIC_tissue_types_affected	"COSMIC_tissue_types_affected"
public static final java.lang.String	FieldName_COSMIC_total_alterations_in_gene	"COSMIC_total_alterations_in_gene"
public static final java.lang.String	FieldName_dbSNP_RS	"dbSNP_RS"
public static final java.lang.String	FieldName_dbSNP_Val_Status	"dbSNP_Val_Status"
public static final java.lang.String	FieldName_Description	"Description"
public static final java.lang.String	FieldName_DNARepairGenes_Activity_linked_to_OMIM	"DNARepairGenes_Activity_linked_to_OMIM"
public static final java.lang.String	FieldName_DrugBank	"DrugBank"
public static final java.lang.String	FieldName_End_Position	"End_Position"
public static final java.lang.String	FieldName_Entrez_Gene_Id	"Entrez_Gene_Id"
public static final java.lang.String	FieldName_FamilialCancerDatabase_Syndromes	"FamilialCancerDatabase_Syndromes"
public static final java.lang.String	FieldName_gc_content	"gc_content"
public static final java.lang.String	FieldName_Genome_Change	"Genome_Change"
public static final java.lang.String	FieldName_GO_Biological_Process	"GO_Biological_Process"
public static final java.lang.String	FieldName_GO_Cellular_Component	"GO_Cellular_Component"
public static final java.lang.String	FieldName_GO_Molecular_Function	"GO_Molecular_Function"
public static final java.lang.String	FieldName_Hugo_Symbol	"Hugo_Symbol"
public static final java.lang.String	FieldName_Match_Norm_Seq_Allele1	"Match_Norm_Seq_Allele1"
public static final java.lang.String	FieldName_Match_Norm_Seq_Allele2	"Match_Norm_Seq_Allele2"
public static final java.lang.String	FieldName_Match_Norm_Validation_Allele1	"Match_Norm_Validation_Allele1"
public static final java.lang.String	FieldName_Match_Norm_Validation_Allele2	"Match_Norm_Validation_Allele2"
public static final java.lang.String	FieldName_Matched_Norm_Sample_Barcode	"Matched_Norm_Sample_Barcode"
public static final java.lang.String	FieldName_Matched_Norm_Sample_UUID	"Matched_Norm_Sample_UUID"
public static final java.lang.String	FieldName_Mutation_Status	"Mutation_Status"
public static final java.lang.String	FieldName_MUTSIG_Published_Results	"MUTSIG_Published_Results"
public static final java.lang.String	FieldName_n_alt_count	"n_alt_count"
public static final java.lang.String	FieldName_n_ref_count	"n_ref_count"
public static final java.lang.String	FieldName_NCBI_Build	"NCBI_Build"
public static final java.lang.String	FieldName_OREGANNO_ID	"OREGANNO_ID"
public static final java.lang.String	FieldName_OREGANNO_Values	"OREGANNO_Values"
public static final java.lang.String	FieldName_Other_Transcripts	"Other_Transcripts"
public static final java.lang.String	FieldName_Protein_Change	"Protein_Change"
public static final java.lang.String	FieldName_ref_context	"ref_context"
public static final java.lang.String	FieldName_Reference_Allele	"Reference_Allele"
public static final java.lang.String	FieldName_Refseq_mRNA_Id	"Refseq_mRNA_Id"
public static final java.lang.String	FieldName_Refseq_prot_Id	"Refseq_prot_Id"
public static final java.lang.String	FieldName_Score	"Score"
public static final java.lang.String	FieldName_Sequence_Source	"Sequence_Source"
public static final java.lang.String	FieldName_Sequencer	"Sequencer"
public static final java.lang.String	FieldName_Sequencing_Phase	"Sequencing_Phase"
public static final java.lang.String	FieldName_Start_Position	"Start_Position"
public static final java.lang.String	FieldName_Strand	"Strand"
public static final java.lang.String	FieldName_SwissProt_acc_Id	"SwissProt_acc_Id"
public static final java.lang.String	FieldName_SwissProt_entry_Id	"SwissProt_entry_Id"
public static final java.lang.String	FieldName_t_alt_count	"t_alt_count"
public static final java.lang.String	FieldName_t_ref_count	"t_ref_count"
public static final java.lang.String	FieldName_TCGAscape_Amplification_Peaks	"TCGAscape_Amplification_Peaks"
public static final java.lang.String	FieldName_TCGAscape_Deletion_Peaks	"TCGAscape_Deletion_Peaks"
public static final java.lang.String	FieldName_Transcript_Exon	"Transcript_Exon"
public static final java.lang.String	FieldName_Transcript_Position	"Transcript_Position"
public static final java.lang.String	FieldName_Transcript_Strand	"Transcript_Strand"
public static final java.lang.String	FieldName_tumor_f	"tumor_f"
public static final java.lang.String	FieldName_Tumor_Sample_Barcode	"Tumor_Sample_Barcode"
public static final java.lang.String	FieldName_Tumor_Sample_UUID	"Tumor_Sample_UUID"
public static final java.lang.String	FieldName_Tumor_Seq_Allele1	"Tumor_Seq_Allele1"
public static final java.lang.String	FieldName_Tumor_Seq_Allele2	"Tumor_Seq_Allele2"
public static final java.lang.String	FieldName_Tumor_Validation_Allele1	"Tumor_Validation_Allele1"
public static final java.lang.String	FieldName_Tumor_Validation_Allele2	"Tumor_Validation_Allele2"
public static final java.lang.String	FieldName_Tumorscape_Amplification_Peaks	"Tumorscape_Amplification_Peaks"
public static final java.lang.String	FieldName_Tumorscape_Deletion_Peaks	"Tumorscape_Deletion_Peaks"
public static final java.lang.String	FieldName_UniProt_AApos	"UniProt_AApos"
public static final java.lang.String	FieldName_UniProt_Experimental_Info	"UniProt_Experimental_Info"
public static final java.lang.String	FieldName_UniProt_Natural_Variations	"UniProt_Natural_Variations"
public static final java.lang.String	FieldName_UniProt_Region	"UniProt_Region"
public static final java.lang.String	FieldName_UniProt_Site	"UniProt_Site"
public static final java.lang.String	FieldName_Validation_Method	"Validation_Method"
public static final java.lang.String	FieldName_Validation_Status	"Validation_Status"
public static final java.lang.String	FieldName_Variant_Classification	"Variant_Classification"
public static final java.lang.String	FieldName_Variant_Type	"Variant_Type"
public static final java.lang.String	FieldName_Verification_Status	"Verification_Status"

org.broadinstitute.hellbender.tools.funcotator.metadata.FuncotationMetadataUtils

Modifier and Type	Constant Field	Value
public static final java.lang.String	UNKNOWN_DESCRIPTION	"Unknown"

org.broadinstitute.hellbender.tools.funcotator.vcfOutput.VcfOutputRenderer

Modifier and Type	Constant Field	Value
public static final java.lang.String	ALL_TRANSCRIPT_DELIMITER	"#"
public static final java.lang.String	DESCRIPTION_PREAMBLE_DELIMITER	": "
public static final java.lang.String	END_TRANSCRIPT_DELIMITER	"]"
public static final java.lang.String	FIELD_DELIMITER	"|"
public static final java.lang.String	FUNCOTATOR_VCF_FIELD_NAME	"FUNCOTATION"
public static final java.lang.String	HEADER_LISTED_FIELD_DELIMITER	"|"
public static final java.lang.String	OTHER_TRANSCRIPT_DELIMITER	"/"
public static final java.lang.String	START_TRANSCRIPT_DELIMITER	"["

org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBArgumentCollection

Modifier and Type	Constant Field	Value
public static final java.lang.String	CALL_GENOTYPES_LONG_NAME	"call-genotypes"
public static final java.lang.String	SHARED_POSIXFS_OPTIMIZATIONS	"genomicsdb-shared-posixfs-optimizations"
public static final java.lang.String	USE_BCF_CODEC_LONG_NAME	"genomicsdb-use-bcf-codec"
public static final java.lang.String	USE_GCS_HDFS_CONNECTOR	"genomicsdb-use-gcs-hdfs-connector"

org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBConstants

Modifier and Type	Constant Field	Value
public static final java.lang.String	DEFAULT_ARRAY_NAME	"genomicsdb_array"
public static final java.lang.String	DEFAULT_CALLSETMAP_FILE_NAME	"callset.json"
public static final java.lang.String	DEFAULT_VCFHEADER_FILE_NAME	"vcfheader.vcf"
public static final java.lang.String	DEFAULT_VIDMAP_FILE_NAME	"vidmap.json"

org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport

Modifier and Type	Constant Field	Value
public static final int	ARRAY_COLUMN_BOUNDS_END	1
public static final int	ARRAY_COLUMN_BOUNDS_START	0
public static final java.lang.String	BATCHSIZE_ARG_LONG_NAME	"batch-size"
public static final java.lang.String	BYPASS_FEATURE_READER	"bypass-feature-reader"
public static final java.lang.String	CONSOLIDATE_ARG_NAME	"consolidate"
public static final java.lang.String	INCREMENTAL_WORKSPACE_ARG_LONG_NAME	"genomicsdb-update-workspace-path"
public static final java.lang.String	INTERVAL_LIST_LONG_NAME	"output-interval-list-to-file"
public static final int	INTERVAL_LIST_SIZE_WARNING_THRESHOLD	100
public static final java.lang.String	MAX_NUM_INTERVALS_TO_IMPORT_IN_PARALLEL	"max-num-intervals-to-import-in-parallel"
public static final java.lang.String	MERGE_CONTIGS_INTO_NUM_PARTITIONS	"merge-contigs-into-num-partitions"
public static final java.lang.String	MERGE_INPUT_INTERVALS_LONG_NAME	"merge-input-intervals"
public static final java.lang.String	OVERWRITE_WORKSPACE_LONG_NAME	"overwrite-existing-genomicsdb-workspace"
public static final java.lang.String	SAMPLE_NAME_MAP_LONG_NAME	"sample-name-map"
public static final java.lang.String	SEGMENT_SIZE_ARG_LONG_NAME	"genomicsdb-segment-size"
public static final java.lang.String	SHARED_POSIXFS_OPTIMIZATIONS	"genomicsdb-shared-posixfs-optimizations"
public static final java.lang.String	USE_GCS_HDFS_CONNECTOR	"genomicsdb-use-gcs-hdfs-connector"
public static final java.lang.String	VALIDATE_SAMPLE_MAP_LONG_NAME	"validate-sample-name-map"
public static final java.lang.String	VCF_BUFFER_SIZE_ARG_NAME	"genomicsdb-vcf-buffer-size"
public static final java.lang.String	VCF_INITIALIZER_THREADS_LONG_NAME	"reader-threads"
public static final java.lang.String	WORKSPACE_ARG_LONG_NAME	"genomicsdb-workspace-path"

org.broadinstitute.hellbender.tools.spark.CreateHadoopBamSplittingIndex

Modifier and Type	Constant Field	Value
public static final java.lang.String	CREATE_BAI_LONG_NAME	"create-bai"
public static final java.lang.String	SPLITTING_INDEX_GRANULARITY_LONG_NAME	"splitting-index-granularity"

org.broadinstitute.hellbender.tools.spark.ParallelCopyGCSDirectoryIntoHDFSSpark

Modifier and Type	Constant Field	Value
public static final java.lang.String	INPUT_GCS_PATH_LONG_NAME	"input-gcs-path"
public static final java.lang.String	INPUT_GLOB	"input-file-glob"
public static final java.lang.String	INPUT_GLOB_ALL_FILES	"*"
public static final java.lang.String	OUTPUT_HDFS_DIRECTORY_LONG_NAME	"output-hdfs-directory"
public static final int	SIXTY_FOUR_MIB	67108864

org.broadinstitute.hellbender.tools.spark.RevertSamSpark

Modifier and Type	Constant Field	Value
public static final java.lang.String	ATTRIBUTE_TO_CLEAR_LONG_NAME	"attributes-to-clear"
public static final java.lang.String	DONT_REMOVE_DUPLICATE_INFORMATION_LONG_NAME	"remove-duplicate-information"
public static final java.lang.String	DONT_RESTORE_ORIGINAL_QUALITIES_LONG_NAME	"dont-restore-original-qualities"
public static final java.lang.String	KEEP_ALIGNMENT_INFORMATION	"keep-alignment-information"
public static final java.lang.String	KEEP_FIRST_DUPLICATE_LONG_NAME	"keep-first-duplicate"
public static final java.lang.String	LIBRARY_NAME_ARG	"library-name"
public static final java.lang.String	OUTPUT_BY_READGROUP_FILE_FORMAT_LONG_NAME	"output-by-readgroup-file-format"
public static final java.lang.String	OUTPUT_BY_READGROUP_LONG_NAME	"output-by-readgroup"
public static final java.lang.String	OUTPUT_MAP_LONG_NAME	"output-map"
public static final java.lang.String	OUTPUT_MAP_OUTPUT_FILE_FIELD_NAME	"OUTPUT"
public static final java.lang.String	OUTPUT_MAP_READ_GROUP_FIELD_NAME	"READ_GROUP_ID"
public static final java.lang.String	REMOVE_DEFAULT_ATTRIBUTE_TO_CLEAR_LONG_NAME	"remove-default-attributes-to-clear"
public static final java.lang.String	SAMPLE_ALIAS_ARG	"sample-alias"

org.broadinstitute.hellbender.tools.spark.bwa.BwaArgumentCollection

Modifier and Type	Constant Field	Value
public static final java.lang.String	BWA_MEM_INDEX_IMAGE_FULL_NAME	"bwa-mem-index-image"
public static final java.lang.String	BWA_MEM_INDEX_IMAGE_SHORT_NAME	"image"
public static final java.lang.String	SINGLE_END_ALIGNMENT_FULL_NAME	"single-end-alignment"
public static final java.lang.String	SINGLE_END_ALIGNMENT_SHORT_NAME	"se"

org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildKmers

Modifier and Type	Constant Field	Value
public static final java.lang.String	BLOOM_FILTER_FALSE_POSITIVE_P_LONG_NAME	"bloom-false-positive-probability"
public static final java.lang.String	BLOOM_FILTER_FALSE_POSITIVE_P_SHORT_NAME	"P"
public static final java.lang.String	KMER_MASK_LONG_NAME	"kmer-mask"
public static final java.lang.String	KMER_MASK_SHORT_NAME	"M"
public static final java.lang.String	KMER_SIZE_LONG_NAME	"kmer-size"
public static final java.lang.String	KMER_SIZE_SHORT_NAME	"SZ"
public static final java.lang.String	KMER_SPACING_LONG_NAME	"kmer-spacing"
public static final java.lang.String	KMER_SPACING_SHORT_NAME	"SP"
public static final java.lang.String	REFERENCE_LONG_NAME	"reference"
public static final java.lang.String	REFERENCE_SHORT_NAME	"R"

org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildReferenceTaxonomy

Modifier and Type	Constant Field	Value
public static final java.lang.String	GENBANK_CATALOG_LONG_NAME	"genbank-catalog"
public static final java.lang.String	GENBANK_CATALOG_SHORT_NAME	"GC"
public static final java.lang.String	MIN_NON_VIRUS_CONTIG_LENGTH_LONG_NAME	"min-non-virus-contig-length"
public static final java.lang.String	MIN_NON_VIRUS_CONTIG_LENGTH_SHORT_NAME	"min-non-virus-contig-length"
public static final java.lang.String	REFSEQ_CATALOG_LONG_NAME	"refseq-catalog"
public static final java.lang.String	REFSEQ_CATALOG_SHORT_NAME	"RC"
public static final java.lang.String	TAX_DUMP_LONG_NAME	"tax-dump"
public static final java.lang.String	TAX_DUMP_SHORT_NAME	"TD"

org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBwaSpark

Modifier and Type	Constant Field	Value
public static final java.lang.String	PAIRED_INPUT_LONG_NAME	"paired-input"
public static final java.lang.String	PAIRED_OUTPUT_LONG_NAME	"paired-output"
public static final java.lang.String	UNPAIRED_INPUT_LONG_NAME	"unpaired-input"
public static final java.lang.String	UNPAIRED_OUTPUT_LONG_NAME	"unpaired-output"

org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqFilterSpark

Modifier and Type	Constant Field	Value
public static final java.lang.String	PAIRED_OUTPUT_LONG_NAME	"paired-output"
public static final java.lang.String	UNPAIRED_OUTPUT_LONG_NAME	"unpaired-output"

org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqPipelineSpark

Modifier and Type	Constant Field	Value
public static final java.lang.String	READS_PER_PARTITION_LONG_NAME	"pipeline-reads-per-partition"

org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqScoreSpark

Modifier and Type	Constant Field	Value
public static final java.lang.String	PAIRED_INPUT_LONG_NAME	"paired-input"
public static final java.lang.String	UNPAIRED_INPUT_LONG_NAME	"unpaired-input"

org.broadinstitute.hellbender.tools.spark.pathseq.PSBwaArgumentCollection

Modifier and Type	Constant Field	Value
public final int	bwaThreads	1
public static final java.lang.String	MAX_ALT_HITS_LONG_NAME	"max-alternate-hits"
public static final java.lang.String	MICROBE_BWA_IMAGE_LONG_NAME	"microbe-bwa-image"
public static final java.lang.String	MICROBE_MIN_SEED_LENGTH_LONG_NAME	"microbe-min-seed-length"
public static final java.lang.String	MICROBE_REF_DICT_LONG_NAME	"microbe-dict"
public static final java.lang.String	SCORE_THRESHOLD_LONG_NAME	"bwa-score-threshold"

org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection

Modifier and Type	Constant Field	Value
public final int	bwaThreads	1
public static final java.lang.String	DUST_MASK_QUALITY_LONG_NAME	"dust-mask-quality"
public static final java.lang.String	DUST_T_SCORE_LONG_NAME	"dust-t"
public static final java.lang.String	DUST_WINDOW_SIZE_LONG_NAME	"dust-window"
public static final java.lang.String	FILTER_BWA_IMAGE_LONG_NAME	"filter-bwa-image"
public static final java.lang.String	FILTER_BWA_SEED_LENGTH_LONG_NAME	"filter-bwa-seed-length"
public static final java.lang.String	FILTER_DUPLICATES_LONG_NAME	"filter-duplicates"
public static final java.lang.String	FILTER_METRICS_FILE_LONG_NAME	"filter-metrics"
public static final java.lang.String	FILTER_READS_PER_PARTITION_LONG_NAME	"filter-reads-per-partition"
public static final java.lang.String	HOST_KMER_COUNT_THRESHOLD_LONG_NAME	"host-kmer-thresh"
public static final java.lang.String	HOST_MIN_IDENTITY_LONG_NAME	"host-min-identity"
public static final java.lang.String	HOST_MIN_IDENTITY_SHORT_NAME	"host-min-identity"
public static final java.lang.String	IGNORE_ALIGNMENT_CONTIGS_LONG_NAME	"ignore-alignment-contigs"
public static final java.lang.String	IGNORE_ALIGNMENT_CONTIGS_SHORT_NAME	"ignore-alignment-contigs"
public static final java.lang.String	IS_HOST_ALIGNED_LONG_NAME	"is-host-aligned"
public static final java.lang.String	KMER_FILE_PATH_LONG_NAME	"kmer-file"
public static final java.lang.String	MAX_ADAPTER_MISMATCHES_LONG_NAME	"max-adapter-mismatches"
public static final java.lang.String	MAX_MASKED_BASES_LONG_NAME	"max-masked-bases"
public static final java.lang.String	MIN_ADAPTER_LENGTH_LONG_NAME	"min-adapter-length"
public static final java.lang.String	MIN_BASE_QUALITY_LONG_NAME	"min-base-quality"
public static final java.lang.String	MIN_CLIPPED_READ_LENGTH_LONG_NAME	"min-clipped-read-length"
public static final java.lang.String	QUALITY_SCORE_THRESHOLD_LONG_NAME	"quality-threshold"
public static final java.lang.String	SKIP_FILTERS_LONG_NAME	"skip-quality-filters"
public static final java.lang.String	SKIP_PRE_BWA_REPARTITION_LONG_NAME	"skip-pre-bwa-repartition"

org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerUtils

Modifier and Type	Constant Field	Value
public static final java.lang.String	BLOOM_FILTER_EXTENSION	".bfi"
public static final java.lang.String	HOPSCOTCH_SET_EXTENSION	".hss"

org.broadinstitute.hellbender.tools.spark.pathseq.PSScoreArgumentCollection

Modifier and Type	Constant Field	Value
public static final java.lang.String	DIVIDE_BY_GENOME_LENGTH_LONG_NAME	"divide-by-genome-length"
public static final java.lang.String	DIVIDE_BY_GENOME_LENGTH_SHORT_NAME	"divide-by-genome-length"
public static final java.lang.String	IDENTITY_MARGIN_LONG_NAME	"identity-margin"
public static final java.lang.String	IDENTITY_MARGIN_SHORT_NAME	"identity-margin"
public static final java.lang.String	MIN_SCORE_IDENTITY_LONG_NAME	"min-score-identity"
public static final java.lang.String	MIN_SCORE_IDENTITY_SHORT_NAME	"min-score-identity"
public static final java.lang.String	NOT_NORMALIZED_BY_KINGDOM_LONG_NAME	"not-normalized-by-kingdom"
public static final java.lang.String	NOT_NORMALIZED_BY_KINGDOM_SHORT_NAME	"not-normalized-by-kingdom"
public static final java.lang.String	SCORE_METRICS_FILE_LONG_NAME	"score-metrics"
public static final java.lang.String	SCORE_METRICS_FILE_SHORT_NAME	"SM"
public static final java.lang.String	SCORE_READS_PER_PARTITION_LONG_NAME	"score-reads-per-partition-estimate"
public static final java.lang.String	SCORE_READS_PER_PARTITION_SHORT_NAME	"score-reads-per-partition-estimate"
public static final java.lang.String	SCORE_WARNINGS_FILE_LONG_NAME	"score-warnings"
public static final java.lang.String	SCORE_WARNINGS_FILE_SHORT_NAME	"SW"
public static final java.lang.String	SCORES_OUTPUT_LONG_NAME	"scores-output"
public static final java.lang.String	SCORES_OUTPUT_SHORT_NAME	"SO"
public static final java.lang.String	TAXONOMIC_DATABASE_LONG_NAME	"taxonomy-file"
public static final java.lang.String	TAXONOMIC_DATABASE_SHORT_NAME	"T"

org.broadinstitute.hellbender.tools.spark.pathseq.PSScorer

Modifier and Type	Constant Field	Value
public static final java.lang.String	HITS_TAG	"YP"
public static final double	SCORE_GENOME_LENGTH_UNITS	1000000.0

org.broadinstitute.hellbender.tools.spark.pathseq.PSTree

Modifier and Type	Constant Field	Value
public static final int	NULL_NODE	0

org.broadinstitute.hellbender.tools.spark.pipelines.metrics.MetricsCollectorSpark<T extends MetricsArgumentCollection>

Modifier and Type	Constant Field	Value
public static final long	serialVersionUID	1L

org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection

Modifier and Type	Constant Field	Value
public static final int	STRUCTURAL_VARIANT_SIZE_LOWER_BOUND	50

org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigAlignmentsArgumentCollection

Modifier and Type	Constant Field	Value
public static final int	ASSEMBLY_ALIGNMENT_MQ_FILTER_DEFAULT	30
public static final int	CHIMERIC_ALIGNMENTS_HIGHMQ_THRESHOLD	60
public static final int	DEFAULT_ASSEMBLED_IMPRECISE_EVIDENCE_OVERLAP_UNCERTAINTY	100
public static final int	DEFAULT_IMPRECISE_VARIANT_EVIDENCE_THRESHOLD	7
public static final int	DEFAULT_MAX_CALLABLE_IMPRECISE_DELETION_SIZE	15000
public static final int	DEFAULT_MIN_ALIGNMENT_LENGTH	50
public static final int	DEFAULT_TRUTH_INTERVAL_PADDING	50
public static final int	GAPPED_ALIGNMENT_BREAK_DEFAULT_SENSITIVITY	50

org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection

Modifier and Type	Constant Field	Value
public static final int	KMER_SIZE	51
public static final int	MAX_DUST_SCORE	49
public static final double	TRAINING_SET_MEAN_COVERAGE	42.855164
public static final int	TRAINING_SET_OPTIMAL_MIN_COHERENCE	7
public static final int	TRAINING_SET_OPTIMAL_MIN_OVERLAP	15

org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoverFromLocalAssemblyContigAlignmentsSpark

Modifier and Type	Constant Field	Value
public static final java.lang.String	COMPLEX_CHIMERA_VCF_FILE_NAME	"Complex.vcf"
public static final java.lang.String	MERGED_VCF_FILE_NAME	"merged_simple.vcf"
public static final java.lang.String	REINTERPRETED_1_SEG_CALL_VCF_FILE_NAME	"cpx_reinterpreted_simple_1_seg.vcf"
public static final java.lang.String	REINTERPRETED_MULTI_SEG_CALL_VCF_FILE_NAME	"cpx_reinterpreted_simple_multi_seg.vcf"
public static final java.lang.String	SIMPLE_CHIMERA_VCF_FILE_NAME	"NonComplex.vcf"

org.broadinstitute.hellbender.tools.spark.sv.discovery.SvType

Modifier and Type	Constant Field	Value
public static final int	NO_APPLICABLE_END	-1
public static final int	NO_APPLICABLE_LEN	-1

org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedContig

Modifier and Type	Constant Field	Value
public static final int	ALIGNMENT_LOW_READ_UNIQUENESS_THRESHOLD	10

org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignmentInterval

Modifier and Type	Constant Field	Value
public static final int	NO_AS	-1
public static final int	NO_NM	-1
public static final java.lang.String	NO_VALUE_STR	"."
public static final java.lang.String	PACKED_STRING_REP_SEPARATOR	"_"
public static final java.lang.String	SA_TAG_FIELD_SEPARATOR	","
public static final java.lang.String	SA_TAG_INTERVAL_SEPARATOR_STR	";"

org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AssemblyContigWithFineTunedAlignments

Modifier and Type	Constant Field	Value
public static final java.lang.String	NO_GOOD_MAPPING_TO_NON_CANONICAL_CHROMOSOME	"NONE"

org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.CpxVariantCanonicalRepresentation

Modifier and Type	Constant Field	Value
public static final java.lang.String	UNMAPPED_INSERTION	"UINS"

org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.CpxVariantInterpreter

Modifier and Type	Constant Field	Value
public static final int	MIN_READ_SPAN_AFTER_DEOVERLAP	2

org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.DiscordantReadPairEvidence

Modifier and Type	Constant Field	Value
public static final int	MATE_ALIGNMENT_LENGTH_UNCERTAINTY	2

org.broadinstitute.hellbender.tools.spark.sv.evidence.FindBadGenomicKmersSpark

Modifier and Type	Constant Field	Value
public static final int	MAX_KMER_FREQ	3
public static final int	REF_RECORD_LEN	10000
public static final int	REF_RECORDS_PER_PARTITION	104

org.broadinstitute.hellbender.tools.spark.sv.evidence.FindBreakpointEvidenceSpark

Modifier and Type	Constant Field	Value
public static final int	DEPTH_WINDOW_SIZE	100000

org.broadinstitute.hellbender.tools.spark.sv.evidence.KSWindowFinder

Modifier and Type	Constant Field	Value
protected static final int	BLOCK_SIZE	250
protected static final float	KS_SIGNIFICANCE	3.100000030826777E-4f
protected static final float	MAX_APPARENT_BASES_PER_WINDOW	625.0f

org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata

Modifier and Type	Constant Field	Value
public static final java.lang.String	CDF_PREFIX	"template size cumulative counts:"

org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.PartitionBounds

Modifier and Type	Constant Field	Value
public static final int	UNMAPPED	2147483647

org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.Serializer

Modifier and Type	Constant Field	Value
public static final java.lang.String	MAGIC_STRING	"9wdgy2yEbw0jg"
public static final java.lang.String	VERSION_STRING	"0.1"

org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants

Modifier and Type	Constant Field	Value
public static final java.lang.String	ALGORITHMS_ATTRIBUTE	"ALGORITHMS"
public static final java.lang.String	ALIGN_LENGTHS	"ALIGN_LENGTHS"
public static final java.lang.String	ASSEMBLY_BASED_VARIANT_ALN_LENGTH_FILTER_KEY	"SHORT_ALN"
public static final java.lang.String	ASSEMBLY_BASED_VARIANT_MQ_FILTER_KEY	"LOW_MQ"
public static final java.lang.String	BND_MATEID_STR	"MATEID"
public static final java.lang.String	BREAKEND_STR	"BND"
public static final java.lang.String	CIEND	"CIEND"
public static final java.lang.String	CIPOS	"CIPOS"
public static final java.lang.String	CLUSTER_MEMBER_IDS_KEY	"MEMBERS"
public static final java.lang.String	CONTIG_NAMES	"CTG_NAMES"
public static final java.lang.String	CONTIG2_ATTRIBUTE	"CHR2"
public static final java.lang.String	COPY_NUMBER_FORMAT	"CN"
public static final java.lang.String	COPY_NUMBER_QUALITY_FORMAT	"CNQ"
public static final java.lang.String	CPX_EVENT_ALT_ARRANGEMENTS	"ALT_ARRANGEMENT"
public static final java.lang.String	CPX_EVENT_KEY	"CPX_EVENT"
public static final java.lang.String	CPX_SV_REF_SEGMENTS	"SEGMENTS"
public static final java.lang.String	CPX_SV_SYB_ALT_ALLELE_STR	"CPX"
public static final java.lang.String	CTG_GOOD_NONCANONICAL_MAPPING	"CTG_GOOD_NONCANONICAL_MAPPING"
public static final java.lang.String	DEPTH_ALGORITHM	"depth"
public static final java.lang.String	DUP_ANNOTATIONS_IMPRECISE	"DUP_ANNOTATIONS_IMPRECISE"
public static final java.lang.String	DUP_IMPRECISE_AFFECTED_RANGE	"DUP_IMPRECISE_AFFECTED_RANGE"
public static final java.lang.String	DUP_INV_INTERNAL_ID_START_STRING	"INS-DUPLICATION-INVERTED-EXPANSION"
public static final java.lang.String	DUP_ORIENTATIONS	"DUP_ORIENTATIONS"
public static final java.lang.String	DUP_REPEAT_UNIT_REF_SPAN	"DUP_REPEAT_UNIT_REF_SPAN"
public static final java.lang.String	DUP_SEQ_CIGARS	"DUP_SEQ_CIGARS"
public static final java.lang.String	DUP_TAN_CONTRACTION_INTERNAL_ID_START_STRING	"DEL-DUPLICATION-TANDEM-CONTRACTION"
public static final java.lang.String	DUP_TAN_CONTRACTION_STRING	"CONTRACTION"
public static final java.lang.String	DUP_TAN_EXPANSION_INTERNAL_ID_START_STRING	"INS-DUPLICATION-TANDEM-EXPANSION"
public static final java.lang.String	DUP_TAN_EXPANSION_STRING	"EXPANSION"
public static final java.lang.String	DUPLICATION_NUMBERS	"DUP_NUM"
public static final java.lang.String	END2_ATTRIBUTE	"END2"
public static final java.lang.String	EXPECTED_COPY_NUMBER_FORMAT	"ECN"
public static final java.lang.String	EXTERNAL_CNV_CALLS	"EXTERNAL_CNV_CALLS"
public static final java.lang.String	FREQUENCY_FILTER_KEY	"FREQ"
public static final java.lang.String	HOMOLOGY	"HOMSEQ"
public static final java.lang.String	HOMOLOGY_LENGTH	"HOMLEN"
public static final java.lang.String	HQ_MAPPINGS	"HQ_MAPPINGS"
public static final java.lang.String	IMPRECISE	"IMPRECISE"
public static final java.lang.String	INSERTED_SEQUENCE	"INSSEQ"
public static final java.lang.String	INSERTED_SEQUENCE_LENGTH	"INSLEN"
public static final java.lang.String	INSERTED_SEQUENCE_MAPPINGS	"INSSEQ_MAP"
public static final java.lang.String	INTERVAL_VARIANT_ID_FIELD_SEPARATOR	"_"
public static final java.lang.String	INV33	"INV33"
public static final java.lang.String	INV55	"INV55"
public static final java.lang.String	LINK	"LINK"
public static final java.lang.String	LOW_QS_SCORE_FILTER_KEY	"LOW_QS"
public static final java.lang.String	MAPPING_QUALITIES	"MAPPING_QUALITIES"
public static final java.lang.String	MAX_ALIGN_LENGTH	"MAX_ALIGN_LENGTH"
public static final java.lang.String	READ_PAIR_SUPPORT	"READ_PAIR_SUPPORT"
public static final java.lang.String	SEQ_ALT_HAPLOTYPE	"SEQ_ALT_HAPLOTYPE"
public static final java.lang.String	SPLIT_READ_SUPPORT	"SPLIT_READ_SUPPORT"
public static final java.lang.String	STRANDS_ATTRIBUTE	"STRANDS"
public static final java.lang.String	SVLEN	"SVLEN"
public static final java.lang.String	SVTYPE	"SVTYPE"
public static final java.lang.String	SYMB_ALT_STRING_DEL	"DEL"
public static final java.lang.String	SYMB_ALT_STRING_DUP	"DUP"
public static final java.lang.String	SYMB_ALT_STRING_INS	"INS"
public static final java.lang.String	SYMB_ALT_STRING_INV	"INV"
public static final java.lang.String	SYMB_ALT_STRING_INVDUP	"DUP:INV"
public static final java.lang.String	TOTAL_MAPPINGS	"TOTAL_MAPPINGS"

org.broadinstitute.hellbender.tools.spark.sv.utils.SVContext

Modifier and Type	Constant Field	Value
public static final int	NO_LENGTH	-1

org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils

Modifier and Type	Constant Field	Value
public static final char	FRAGMENT_NUMBER_SEPARATOR_CHR	47
public static final char	HEADER_FIELD_EQUAL_CHR	61
public static final java.lang.String	HEADER_FIELD_LIST_SEPARATOR_STR	";"
public static final char	HEADER_FIELD_SEPARATOR_CHR	9
public static final java.lang.String	HEADER_FIELD_SEPARATOR_REGEXP	"\\t"
public static final char	HEADER_PREFIX_CHR	64

org.broadinstitute.hellbender.tools.spark.sv.utils.SVUtils

Modifier and Type	Constant Field	Value
public static final java.lang.String	GATKSV_CONTIG_ALIGNMENTS_READ_GROUP_ID	"GATKSVContigAlignments"

org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.MarkDuplicatesSpark

Modifier and Type	Constant Field	Value
public static final java.lang.String	ALLOW_MULTIPLE_SORT_ORDERS_IN_INPUT_ARG	"allow-multiple-sort-orders-in-input"
public static final java.lang.String	TREAT_UNSORTED_AS_ORDERED	"treat-unsorted-as-querygroup-ordered"

org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.MarkDuplicatesSparkUtils

Modifier and Type	Constant Field	Value
public static final java.lang.String	OPTICAL_DUPLICATE_TOTAL_ATTRIBUTE_NAME	"OD"

org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark

Modifier and Type	Constant Field	Value
public static final java.lang.String	INPUT_2_LONG_NAME	"input2"
public static final java.lang.String	INPUT_2_SHORT_NAME	"I2"
public static final java.lang.String	PRINT_SUMMARY_LONG_NAME	"print-summary"
public static final java.lang.String	THROW_ON_DIFF_LONG_NAME	"throw-on-diff"

org.broadinstitute.hellbender.tools.sv.BafEvidence

Modifier and Type	Constant Field	Value
public static final java.lang.String	BCI_VERSION	"1.0"

org.broadinstitute.hellbender.tools.sv.DepthEvidence

Modifier and Type	Constant Field	Value
public static final java.lang.String	BCI_VERSION	"1.0"

org.broadinstitute.hellbender.tools.sv.DiscordantPairEvidence

Modifier and Type	Constant Field	Value
public static final java.lang.String	BCI_VERSION	"1.0"

org.broadinstitute.hellbender.tools.sv.LocusDepth

Modifier and Type	Constant Field	Value
public static final java.lang.String	BCI_VERSION	"1.0"

org.broadinstitute.hellbender.tools.sv.PrintSVEvidence<F extends htsjdk.tribble.Feature>

Modifier and Type	Constant Field	Value
public static final java.lang.String	COMPRESSION_LEVEL_NAME	"compression-level"
public static final java.lang.String	EVIDENCE_FILE_NAME	"evidence-file"

org.broadinstitute.hellbender.tools.sv.SplitReadEvidence

Modifier and Type	Constant Field	Value
public static final java.lang.String	BCI_VERSION	"1.0"

org.broadinstitute.hellbender.tools.sv.SVCallRecord

Modifier and Type	Constant Field	Value
public static final java.lang.String	STRAND_MINUS	"-"
public static final java.lang.String	STRAND_PLUS	"+"
public static final int	UNDEFINED_LENGTH	-1

org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVLinkage<T extends SVCallRecord>

Modifier and Type	Constant Field	Value
public static final double	DEFAULT_RECIPROCAL_OVERLAP_DEPTH_ONLY	0.8
public static final double	DEFAULT_RECIPROCAL_OVERLAP_MIXED	0.8
public static final double	DEFAULT_RECIPROCAL_OVERLAP_PESR	0.5
public static final double	DEFAULT_SAMPLE_OVERLAP_DEPTH_ONLY	0.0
public static final double	DEFAULT_SAMPLE_OVERLAP_MIXED	0.0
public static final double	DEFAULT_SAMPLE_OVERLAP_PESR	0.0
public static final int	DEFAULT_WINDOW_DEPTH_ONLY	0
public static final int	DEFAULT_WINDOW_MIXED	1000
public static final int	DEFAULT_WINDOW_PESR	500
public static final int	INSERTION_ASSUMED_LENGTH_FOR_OVERLAP	50

org.broadinstitute.hellbender.tools.sv.cluster.CNVLinkage

Modifier and Type	Constant Field	Value
public static final double	DEFAULT_PADDING_FRACTION	0.25
public static final double	DEFAULT_SAMPLE_OVERLAP	0.8

org.broadinstitute.hellbender.tools.validation.CompareBaseQualities

Modifier and Type	Constant Field	Value
public static final java.lang.String	ROUND_DOWN_QUANTIZED_LONG_NAME	"round-down-quantized"
public static final java.lang.String	STATIC_QUANTIZED_QUALS_LONG_NAME	"static-quantized-quals"
public static final java.lang.String	THROW_ON_DIFF_LONG_NAME	"throw-on-diff"

org.broadinstitute.hellbender.tools.validation.CompareMatrix

Modifier and Type	Constant Field	Value
public static final int	dimension	94

org.broadinstitute.hellbender.tools.walkers.CombineGVCFs

Modifier and Type	Constant Field	Value
public static final java.lang.String	ALLELE_FRACTION_DELTA_LONG_NAME	"allele-fraction-error"
public static final java.lang.String	BP_RES_LONG_NAME	"convert-to-base-pair-resolution"
public static final java.lang.String	BREAK_BANDS_LONG_NAME	"break-bands-at-multiples-of"
public static final java.lang.String	DROP_SOMATIC_FILTERING_ANNOTATIONS_LONG_NAME	"drop-somatic-filtering-annotations"
public static final java.lang.String	SOMATIC_INPUT_LONG_NAME	"input-is-somatic"

org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs

Modifier and Type	Constant Field	Value
public static final java.lang.String	ALL_SITES_LONG_NAME	"include-non-variant-sites"
public static final java.lang.String	ALL_SITES_SHORT_NAME	"all-sites"
public static final java.lang.String	FORCE_OUTPUT_INTERVALS_NAME	"force-output-intervals"
public static final java.lang.String	KEEP_COMBINED_LONG_NAME	"keep-combined-raw-annotations"
public static final java.lang.String	KEEP_COMBINED_SHORT_NAME	"keep-combined"
public static final java.lang.String	ONLY_OUTPUT_CALLS_STARTING_IN_INTERVALS_FULL_NAME	"only-output-calls-starting-in-intervals"
public static final java.lang.String	PHASED_HOM_VAR_STRING	"1|1"

org.broadinstitute.hellbender.tools.walkers.SplitIntervals

Modifier and Type	Constant Field	Value
public static final java.lang.String	DEFAULT_EXTENSION	"-scattered.interval_list"
public static final int	DEFAULT_NUMBER_OF_DIGITS	4
public static final java.lang.String	DEFAULT_PREFIX	""
public static final java.lang.String	DONT_MIX_CONTIGS_LONG_NAME	"dont-mix-contigs"
public static final java.lang.String	INTERVAL_FILE_EXTENSION_FULL_NAME	"extension"
public static final java.lang.String	INTERVAL_FILE_PREFIX_FULL_NAME	"interval-file-prefix"
public static final java.lang.String	INTERVAL_NUMBER_OF_DIGITS_FULL_NAME	"interval-file-num-digits"
public static final java.lang.String	MIN_CONTIG_SIZE_LONG_NAME	"min-contig-size"
public static final java.lang.String	PICARD_INTERVAL_FILE_EXTENSION	"interval_list"
public static final java.lang.String	SCATTER_COUNT_LONG_NAME	"scatter-count"
public static final java.lang.String	SCATTER_COUNT_SHORT_NAME	"scatter"
public static final java.lang.String	SUBDIVISION_MODE_lONG_NAME	"subdivision-mode"
public static final java.lang.String	SUBDIVISION_MODE_SHORT_NAME	"mode"

org.broadinstitute.hellbender.tools.walkers.annotator.AnnotationUtils

Modifier and Type	Constant Field	Value
public static final java.lang.String	ALLELE_SPECIFIC_RAW_DELIM	"|"
public static final java.lang.String	ALLELE_SPECIFIC_REDUCED_DELIM	","
public static final java.lang.String	ALLELE_SPECIFIC_SPLIT_REGEX	"\\|"
public static final java.lang.String	BRACKET_REGEX	"\\[|\\]"
public static final java.lang.String	LIST_DELIMITER	","

org.broadinstitute.hellbender.tools.walkers.annotator.BaseQualityHistogram

Modifier and Type	Constant Field	Value
public static final java.lang.String	KEY	"BQHIST"

org.broadinstitute.hellbender.tools.walkers.annotator.ExcessHet

Modifier and Type	Constant Field	Value
public static final int	NUMBER_OF_GENOTYPE_COUNTS	3

org.broadinstitute.hellbender.tools.walkers.annotator.FeaturizedReadSets

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_BASE_QUALITY	25

org.broadinstitute.hellbender.tools.walkers.annotator.OriginalAlignment

Modifier and Type	Constant Field	Value
public static final java.lang.String	KEY	"OCM"

org.broadinstitute.hellbender.tools.walkers.annotator.PossibleDeNovo

Modifier and Type	Constant Field	Value
public static final double	DEFAULT_MIN_GENOTYPE_QUALITY_P	0.0

org.broadinstitute.hellbender.tools.walkers.annotator.RankSumTest

Modifier and Type	Constant Field	Value
protected static final double	INVALID_ELEMENT_FROM_READ	-1d/0d

org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality

Modifier and Type	Constant Field	Value
public static final java.lang.String	RMS_MAPPING_QUALITY_OLD_BEHAVIOR_OVERRIDE_ARGUMENT	"allow-old-rms-mapping-quality-annotation-data"

org.broadinstitute.hellbender.tools.walkers.annotator.StrandBiasTest

Modifier and Type	Constant Field	Value
protected static final int	ARRAY_DIM	2
protected static final int	ARRAY_SIZE	4

org.broadinstitute.hellbender.tools.walkers.annotator.UniqueAltReadCount

Modifier and Type	Constant Field	Value
public static final java.lang.String	KEY	"AS_UNIQ_ALT_READ_COUNT"

org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotator

Modifier and Type	Constant Field	Value
public static final java.lang.String	EXPRESSION_LONG_NAME	"expression"
public static final java.lang.String	EXPRESSION_SHORT_NAME	"E"

org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_InbreedingCoeff

Modifier and Type	Constant Field	Value
public static final int	MIN_SAMPLES	10

org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_RankSumTest

Modifier and Type	Constant Field	Value
public static final java.lang.String	RAW_DELIM	","

org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_StrandBiasTest

Modifier and Type	Constant Field	Value
public static final int	FORWARD	0
public static final int	MIN_COUNT	2
public static final double	MIN_PVALUE	1.0E-320
public static final java.lang.String	PRINT_DELIM	"|"
public static final java.lang.String	REDUCED_DELIM	","
public static final int	REVERSE	1
public static final java.lang.String	SPLIT_DELIM	"\\|"

org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.StrandBiasUtils

Modifier and Type	Constant Field	Value
public static final int	FORWARD	0
public static final int	MIN_COUNT	2
public static final int	REVERSE	1

org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator

Modifier and Type	Constant Field	Value
public static final java.lang.String	KNOWN_SITES_ARG_FULL_NAME	"known-sites"
public static final java.lang.String	USAGE_ONE_LINE_SUMMARY	"Generates recalibration table for Base Quality Score Recalibration (BQSR)"
public static final java.lang.String	USAGE_SUMMARY	"First pass of the Base Quality Score Recalibration (BQSR) -- Generates recalibration table based on various user-specified covariates (such as read group, reported quality score, machine cycle, and nucleotide context)."

org.broadinstitute.hellbender.tools.walkers.consensus.DownsampleByDuplicateSet

Modifier and Type	Constant Field	Value
public static final java.lang.String	FRACTION_TO_KEEP_NAME	"fraction-to-keep"

org.broadinstitute.hellbender.tools.walkers.consensus.ReadsWithSameUMI

Modifier and Type	Constant Field	Value
public static final java.lang.String	FGBIO_MI_TAG_DELIMITER	"/"

org.broadinstitute.hellbender.tools.walkers.contamination.CalculateContamination

Modifier and Type	Constant Field	Value
public static final java.lang.String	HIGH_COVERAGE_RATIO_THRESHOLD_NAME	"high-coverage-ratio-threshold"
public static final java.lang.String	LOW_COVERAGE_RATIO_THRESHOLD_NAME	"low-coverage-ratio-threshold"
public static final java.lang.String	MATCHED_NORMAL_LONG_NAME	"matched-normal"
public static final java.lang.String	MATCHED_NORMAL_SHORT_NAME	"matched"
public static final java.lang.String	TUMOR_SEGMENTATION_LONG_NAME	"tumor-segmentation"
public static final java.lang.String	TUMOR_SEGMENTATION_SHORT_NAME	"segments"

org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationModel

Modifier and Type	Constant Field	Value
public static final int	HOM_ALT	3
public static final int	HOM_REF	0
public static final double	INITIAL_MAF_THRESHOLD	0.4
public static final double	MAF_STEP_SIZE	0.04
public static final double	MAF_TO_SWITCH_TO_HOM_REF	0.25
public static final double	MAF_TO_SWITCH_TO_UNSCRUPULOUS_HOM_REF	0.2
public static final double	MINIMUM_UNSCRUPULOUS_HOM_REF_ALT_FRACTION_THRESHOLD	0.1
public static final double	UNSCRUPULOUS_HOM_REF_ALLELE_FRACTION	0.15
public static final double	UNSCRUPULOUS_HOM_REF_FRACTION_TO_REMOVE_FOR_POSSIBLE_LOH	0.1
public static final double	UNSCRUPULOUS_HOM_REF_PERCENTILE	90.0

org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationSegmenter

Modifier and Type	Constant Field	Value
public static final int	KERNEL_SEGMENTER_DIMENSION	100
public static final double	KERNEL_SEGMENTER_LINEAR_COST	1.0
public static final double	KERNEL_SEGMENTER_LOG_LINEAR_COST	1.0
public static final int	MAX_CHANGEPOINTS_PER_CHROMOSOME	10
public static final int	POINTS_PER_SEGMENTATION_WINDOW	50

org.broadinstitute.hellbender.tools.walkers.contamination.GetPileupSummaries

Modifier and Type	Constant Field	Value
public static final java.lang.String	MAX_SITE_AF_LONG_NAME	"maximum-population-allele-frequency"
public static final java.lang.String	MAX_SITE_AF_SHORT_NAME	"max-af"
public static final java.lang.String	MIN_MAPPING_QUALITY_LONG_NAME	"min-mapping-quality"
public static final java.lang.String	MIN_MAPPING_QUALITY_SHORT_NAME	"mmq"
public static final java.lang.String	MIN_SITE_AF_LONG_NAME	"minimum-population-allele-frequency"
public static final java.lang.String	MIN_SITE_AF_SHORT_NAME	"min-af"

org.broadinstitute.hellbender.tools.walkers.fasta.FastaAlternateReferenceMaker

Modifier and Type	Constant Field	Value
public static final java.lang.String	SNP_MASK_LONG_NAME	"snp-mask"
public static final java.lang.String	SNP_MASK_PRIORITY_LONG_NAME	"snp-mask-priority"
public static final java.lang.String	USE_IUPAC_SAMPLE_LONG_NAME	"use-iupac-sample"

org.broadinstitute.hellbender.tools.walkers.fasta.FastaReferenceMaker

Modifier and Type	Constant Field	Value
public static final java.lang.String	LINE_WIDTH_LONG_NAME	"line-width"

org.broadinstitute.hellbender.tools.walkers.fasta.ShiftFasta

Modifier and Type	Constant Field	Value
public static final java.lang.String	INTERAL_FILE_NAME	"interval-file-name"
public static final java.lang.String	LINE_WIDTH_LONG_NAME	"line-width"
public static final java.lang.String	SHIFT_BACK_OUTPUT	"shift-back-output"
public static final java.lang.String	SHIFT_OFFSET_LIST	"shift-offset-list"

org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration

Modifier and Type	Constant Field	Value
public static final java.lang.String	ALLELE_SPECIFIC_LONG_NAME	"apply-allele-specific-filters"
public static final java.lang.String	CLUSTER_SIZE_LONG_NAME	"cluster-size"
public static final java.lang.String	CLUSTER_WINDOW_SIZE_LONG_NAME	"cluster-window-size"
public static final java.lang.String	CLUSTERED_SNP_FILTER_NAME	"SnpCluster"
public static final java.lang.String	FILTER_EXPRESSION_LONG_NAME	"filter-expression"
public static final java.lang.String	FILTER_NAME_LONG_NAME	"filter-name"
public static final java.lang.String	FILTER_NOT_IN_MASK_LONG_NAME	"filter-not-in-mask"
public static final java.lang.String	GENOTYPE_FILTER_EXPRESSION_LONG_NAME	"genotype-filter-expression"
public static final java.lang.String	GENOTYPE_FILTER_NAME_LONG_NAME	"genotype-filter-name"
public static final java.lang.String	INVERT_GT_LONG_NAME	"invert-genotype-filter-expression"
public static final java.lang.String	INVERT_LONG_NAME	"invert-filter-expression"
public static final java.lang.String	MASK_EXTENSION_LONG_NAME	"mask-extension"
public static final java.lang.String	MASK_NAME_LONG_NAME	"mask-name"
public static final java.lang.String	MISSING_VAL_LONG_NAME	"missing-values-evaluate-as-failing"
public static final java.lang.String	NO_CALL_GTS_LONG_NAME	"set-filtered-genotype-to-no-call"

org.broadinstitute.hellbender.tools.walkers.genotyper.AlleleSubsettingUtils

Modifier and Type	Constant Field	Value
public static final int	NUM_OF_STRANDS	2

org.broadinstitute.hellbender.tools.walkers.genotyper.DRAGENGenotypesModel

Modifier and Type	Constant Field	Value
public static final double	BQD_HOMOPOLYMER_PHRED_ADJUSTMENT_FACTOR	5.0
public static final double	FLAT_SNP_HET_PRIOR	34.77

org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeCalculationArgumentCollection

Modifier and Type	Constant Field	Value
public static final java.lang.String	CALL_CONFIDENCE_LONG_NAME	"standard-min-confidence-threshold-for-calling"
public static final java.lang.String	CALL_CONFIDENCE_SHORT_NAME	"stand-call-conf"
public static final int	DEFAULT_MAX_ALTERNATE_ALLELES	6
public static final int	DEFAULT_MAX_GENOTYPE_COUNT	1024
public static final double	DEFAULT_STANDARD_CONFIDENCE_FOR_CALLING	30.0
public static final java.lang.String	MAX_ALTERNATE_ALLELES_LONG_NAME	"max-alternate-alleles"
public static final java.lang.String	MAX_GENOTYPE_COUNT_LONG_NAME	"max-genotype-count"
public static final java.lang.String	NUM_REF_SAMPLES_LONG_NAME	"num-reference-samples-if-no-call"
public static final java.lang.String	SAMPLE_PLOIDY_LONG_NAME	"sample-ploidy"
public static final java.lang.String	SAMPLE_PLOIDY_SHORT_NAME	"ploidy"
public static final java.lang.String	SUPPORTING_CALLSET_LONG_NAME	"population-callset"
public static final java.lang.String	SUPPORTING_CALLSET_SHORT_NAME	"population"

org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeLikelihoodCalculators

Modifier and Type	Constant Field	Value
public static final int	MAXIMUM_STRONG_REF_GENOTYPE_PER_PLOIDY	1000

org.broadinstitute.hellbender.tools.walkers.genotyper.StandardCallerArgumentCollection

Modifier and Type	Constant Field	Value
public static final double	DEFAULT_CONTAMINATION_FRACTION	0.0

org.broadinstitute.hellbender.tools.walkers.gnarlyGenotyper.GnarlyGenotyper

Modifier and Type	Constant Field	Value
public static final int	PIPELINE_MAX_ALT_COUNT	6

org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection

Modifier and Type	Constant Field	Value
public static final java.lang.String	ALLELE_EXTENSION_LONG_NAME	"allele-informative-reads-overlap-margin"
public static final java.lang.String	BAM_OUTPUT_LONG_NAME	"bam-output"
public static final java.lang.String	BAM_OUTPUT_SHORT_NAME	"bamout"
public static final java.lang.String	BAM_WRITER_TYPE_LONG_NAME	"bam-writer-type"
public static final java.lang.String	DO_NOT_RUN_PHYSICAL_PHASING_LONG_NAME	"do-not-run-physical-phasing"
public static final java.lang.String	DONT_USE_SOFT_CLIPPED_BASES_LONG_NAME	"dont-use-soft-clipped-bases"
public static final java.lang.String	EMIT_REF_CONFIDENCE_LONG_NAME	"emit-ref-confidence"
public static final java.lang.String	EMIT_REF_CONFIDENCE_SHORT_NAME	"ERC"
public static final java.lang.String	FORCE_CALL_ALLELES_LONG_NAME	"alleles"
public static final java.lang.String	FORCE_CALL_FILTERED_ALLELES_LONG_NAME	"force-call-filtered-alleles"
public static final java.lang.String	FORCE_CALL_FILTERED_ALLELES_SHORT_NAME	"genotype-filtered-alleles"
public static final java.lang.String	MAX_MNP_DISTANCE_LONG_NAME	"max-mnp-distance"
public static final java.lang.String	MAX_MNP_DISTANCE_SHORT_NAME	"mnp-dist"
public static final java.lang.String	MIN_BASE_QUALITY_SCORE_LONG_NAME	"min-base-quality-score"
public static final java.lang.String	SMITH_WATERMAN_DANGLING_END_GAP_EXTEND_PENALTY_LONG_NAME	"smith-waterman-dangling-end-gap-extend-penalty"
public static final java.lang.String	SMITH_WATERMAN_DANGLING_END_GAP_OPEN_PENALTY_LONG_NAME	"smith-waterman-dangling-end-gap-open-penalty"
public static final java.lang.String	SMITH_WATERMAN_DANGLING_END_MATCH_VALUE_LONG_NAME	"smith-waterman-dangling-end-match-value"
public static final java.lang.String	SMITH_WATERMAN_DANGLING_END_MISMATCH_PENALTY_LONG_NAME	"smith-waterman-dangling-end-mismatch-penalty"
public static final java.lang.String	SMITH_WATERMAN_HAPLOTYPE_TO_REFERENCE_GAP_EXTEND_PENALTY_LONG_NAME	"smith-waterman-haplotype-to-reference-gap-extend-penalty"
public static final java.lang.String	SMITH_WATERMAN_HAPLOTYPE_TO_REFERENCE_GAP_OPEN_PENALTY_LONG_NAME	"smith-waterman-haplotype-to-reference-gap-open-penalty"
public static final java.lang.String	SMITH_WATERMAN_HAPLOTYPE_TO_REFERENCE_MATCH_VALUE_LONG_NAME	"smith-waterman-haplotype-to-reference-match-value"
public static final java.lang.String	SMITH_WATERMAN_HAPLOTYPE_TO_REFERENCE_MISMATCH_PENALTY_LONG_NAME	"smith-waterman-haplotype-to-reference-mismatch-penalty"
public static final java.lang.String	SMITH_WATERMAN_LONG_NAME	"smith-waterman"
public static final java.lang.String	SMITH_WATERMAN_READ_TO_HAPLOTYPE_GAP_EXTEND_PENALTY_LONG_NAME	"smith-waterman-read-to-haplotype-gap-extend-penalty"
public static final java.lang.String	SMITH_WATERMAN_READ_TO_HAPLOTYPE_GAP_OPEN_PENALTY_LONG_NAME	"smith-waterman-read-to-haplotype-gap-open-penalty"
public static final java.lang.String	SMITH_WATERMAN_READ_TO_HAPLOTYPE_MATCH_VALUE_LONG_NAME	"smith-waterman-read-to-haplotype-match-value"
public static final java.lang.String	SMITH_WATERMAN_READ_TO_HAPLOTYPE_MISMATCH_PENALTY_LONG_NAME	"smith-waterman-read-to-haplotype-mismatch-penalty"
public static final java.lang.String	USE_FILTERED_READS_FOR_ANNOTATIONS_LONG_NAME	"use-filtered-reads-for-annotations"

org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerUtils

Modifier and Type	Constant Field	Value
public static final java.lang.String	ALIGNMENT_REGION_TAG	"AR"
public static final java.lang.String	CALLABLE_REGION_TAG	"CR"
public static final int	MINIMUM_READ_LENGTH_AFTER_TRIMMING	10
public static final int	NUM_HAPLOTYPES_TO_INJECT_FORCE_CALLING_ALLELES_INTO	5
public static final java.lang.String	READ_ORIGINAL_ALIGNMENT_KEY	"originalAlignment"
public static final java.lang.String	SUPPORTED_ALLELES_TAG	"XA"

org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection

Modifier and Type	Constant Field	Value
public static final java.lang.String	DO_NOT_CORRECT_OVERLAPPING_BASE_QUALITIES_LONG_NAME	"do-not-correct-overlapping-quality"
public static final java.lang.String	DRAGEN_GATK_MODE_LONG_NAME	"dragen-mode"
public static final java.lang.String	GQ_BAND_LONG_NAME	"gvcf-gq-bands"
public static final java.lang.String	GQ_BAND_SHORT_NAME	"GQB"
public static final java.lang.String	OUTPUT_BLOCK_LOWER_BOUNDS	"floor-blocks"

org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_READ_QUALITY_FILTER_THRESHOLD	20
public static final byte	MIN_TAIL_QUALITY_WITH_ERROR_CORRECTION	6

org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LikelihoodEngineArgumentCollection

Modifier and Type	Constant Field	Value
public static final java.lang.String	BASE_QUALITY_SCORE_THRESHOLD_FULLNAME	"base-quality-score-threshold"
public static final java.lang.String	DONT_USE_DRAGSTR_PAIRHMM_FULLNAME	"dont-use-dragstr-pair-hmm-scores"
public static final java.lang.String	DRAGSTR_HET_HOM_RATIO_FULLNAME	"dragstr-het-hom-ratio"
public static final java.lang.String	DRAGSTR_PARAMS_PATH_FULLNAME	"dragstr-params-path"

org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine

Modifier and Type	Constant Field	Value
public static final double	DEFAULT_EXPECTED_ERROR_RATE_PER_BASE	0.02
public static final java.lang.String	HMM_BASE_QUALITIES_TAG	"HMMQuals"

org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection

Modifier and Type	Constant Field	Value
public static final java.lang.String	CAPTURE_ASSEMBLY_FAILURE_BAM_LONG_NAME	"capture-assembly-failure-bam"
public static final java.lang.String	DONT_INCREASE_KMER_SIZE_LONG_NAME	"dont-increase-kmer-sizes-for-cycles"
public static final java.lang.String	ERROR_CORRECT_READS_LONG_NAME	"error-correct-reads"
public static final java.lang.String	KMER_SIZE_LONG_NAME	"kmer-size"
public static final java.lang.String	LINKED_DE_BRUIJN_GRAPH_LONG_NAME	"linked-de-bruijn-graph"
public static final java.lang.String	PILEUP_ERROR_CORRECTION_LOG_ODDS_NAME	"error-correction-log-odds"

org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceModel

Modifier and Type	Constant Field	Value
public static final java.lang.String	INDEL_INFORMATIVE_BASES_CACHE_ATTRIBUTE_NAME	"IDL"
protected static final int	MAX_N_INDEL_INFORMATIVE_READS	40
protected static final java.lang.String	NON_REF_ALLELE_DESCRIPTION	"Represents any possible alternative allele not already represented at this location by REF and ALT"
public static final boolean	USE_CACHED_READ_INDEL_INFORMATIVENESS_VALUES	true

org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.JunctionTreeKBestHaplotypeFinder<V extends BaseVertex,E extends BaseEdge>

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_MAX_ACCEPTABLE_DECISION_EDGES_WITHOUT_JT_GUIDANCE	5
public static final int	DEFAULT_MAX_ACCEPTABLE_REPETITIONS_OF_A_KMER_IN_A_PATH	1
public static final int	DEFAULT_MAX_PATHS_TO_CONSIDER_WITHOUT_RESULT	1000
public static final int	DEFAULT_MAX_PATHS_TO_EVER_CONSIDER	10000
public static final int	DEFAULT_MAX_UPSTREAM_REFERENCE_JUMP_TO_ALLOW	40
public static final int	DEFAULT_MINIMUM_WEIGHT_FOR_JT_BRANCH_TO_NOT_BE_PRUNED	1
public static final int	DEFAULT_NUM_UPSTREAM_REFERENCE_EDGES_TO_TOLERATE	10
public static final int	DEFAULT_OUTGOING_JT_EVIDENCE_THRESHOLD_TO_BELEIVE	3

org.broadinstitute.hellbender.tools.walkers.mutect.CreateSomaticPanelOfNormals

Modifier and Type	Constant Field	Value
public static final java.lang.String	BETA_SHAPE_INFO_FIELD	"BETA"
public static final double	DEFAULT_MAX_GERMLINE_PROBABILITY	0.5
public static final int	DEFAULT_MIN_SAMPLE_COUNT	2
public static final java.lang.String	FRACTION_INFO_FIELD	"FRACTION"
public static final java.lang.String	MAX_GERMLINE_PROBABILITY_LONG_NAME	"max-germline-probability"
public static final java.lang.String	MIN_SAMPLE_COUNT_LONG_NAME	"min-sample-count"

org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection

Modifier and Type	Constant Field	Value
public static final java.lang.String	CALLABLE_DEPTH_LONG_NAME	"callable-depth"
public static final double	DEFAULT_AF_FOR_MITO_CALLING	0.004
public static final double	DEFAULT_AF_FOR_TUMOR_NORMAL_CALLING	1.0E-6
public static final double	DEFAULT_AF_FOR_TUMOR_ONLY_CALLING	5.0E-8
public static final java.lang.String	DEFAULT_AF_LONG_NAME	"af-of-alleles-not-in-resource"
public static final java.lang.String	DEFAULT_AF_SHORT_NAME	"default-af"
public static final int	DEFAULT_CALLABLE_DEPTH	10
public static final double	DEFAULT_EMISSION_LOG_10_ODDS	3.0
public static final double	DEFAULT_GVCF_LOG_10_ODDS	-1d/0d
public static final double	DEFAULT_INITIAL_LOG_10_ODDS	2.0
public static final double	DEFAULT_MITO_EMISSION_LOD	0.0
public static final double	DEFAULT_MITO_INITIAL_LOG_10_ODDS	0.0
public static final double	DEFAULT_NORMAL_LOG_10_ODDS	2.2
public static final java.lang.String	DOWNSAMPLING_STRIDE_LONG_NAME	"downsampling-stride"
public static final java.lang.String	DOWNSAMPLING_STRIDE_SHORT_NAME	"stride"
public static final java.lang.String	EMISSION_LOD_LONG_NAME	"tumor-lod-to-emit"
public static final java.lang.String	EMISSION_LOG_SHORT_NAME	"emit-lod"
public static final java.lang.String	F1R2_TAR_GZ_NAME	"f1r2-tar-gz"
public static final java.lang.String	GENOTYPE_GERMLINE_SITES_LONG_NAME	"genotype-germline-sites"
public static final java.lang.String	GENOTYPE_PON_SITES_LONG_NAME	"genotype-pon-sites"
public static final java.lang.String	GERMLINE_RESOURCE_LONG_NAME	"germline-resource"
public static final java.lang.String	IGNORE_ITR_ARTIFACTS_LONG_NAME	"ignore-itr-artifacts"
public static final java.lang.String	INDEPENDENT_MATES_LONG_NAME	"independent-mates"
public static final java.lang.String	INITIAL_TUMOR_LOG_10_ODDS_LONG_NAME	"initial-tumor-lod"
public static final java.lang.String	INITIAL_TUMOR_LOG_10_ODDS_SHORT_NAME	"init-lod"
public static final java.lang.String	LOD_BAND_LONG_NAME	"gvcf-lod-band"
public static final java.lang.String	LOD_BAND_SHORT_NAME	"LODB"
public static final java.lang.String	MAX_POPULATION_AF_LONG_NAME	"max-population-af"
public static final java.lang.String	MAX_POPULATION_AF_SHORT_NAME	"max-af"
public static final java.lang.String	MAX_SUSPICIOUS_READS_PER_ALIGNMENT_START_LONG_NAME	"max-suspicious-reads-per-alignment-start"
public static final java.lang.String	MICROBIAL_MODE_LONG_NAME	"microbial-mode"
public static final java.lang.String	MINIMUM_ALLELE_FRACTION_LONG_NAME	"minimum-allele-fraction"
public static final java.lang.String	MINIMUM_ALLELE_FRACTION_SHORT_NAME	"min-AF"
public static final java.lang.String	MITOCHONDRIA_MODE_LONG_NAME	"mitochondria-mode"
public static final java.lang.String	NORMAL_LOG_10_ODDS_LONG_NAME	"normal-lod"
public static final java.lang.String	NORMAL_SAMPLE_LONG_NAME	"normal-sample"
public static final java.lang.String	NORMAL_SAMPLE_SHORT_NAME	"normal"
public static final java.lang.String	PANEL_OF_NORMALS_LONG_NAME	"panel-of-normals"
public static final java.lang.String	PANEL_OF_NORMALS_SHORT_NAME	"pon"
public static final java.lang.String	PCR_INDEL_QUAL_LONG_NAME	"pcr-indel-qual"
public static final java.lang.String	PCR_SNV_QUAL_LONG_NAME	"pcr-snv-qual"
public static final java.lang.String	TRAINING_DATA_MODE_LONG_NAME	"training-data-mode"
public static final java.lang.String	TRAINING_DATA_MODE_REF_DOWNSAMPLE_LONG_NAME	"training-data-mode-ref-downsample"
public static final java.lang.String	TUMOR_SAMPLE_LONG_NAME	"tumor-sample"
public static final java.lang.String	TUMOR_SAMPLE_SHORT_NAME	"tumor"

org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2

Modifier and Type	Constant Field	Value
public static final java.lang.String	DEFAULT_STATS_EXTENSION	".stats"
public static final java.lang.String	MUTECT_STATS_SHORT_NAME	"stats"

org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2Engine

Modifier and Type	Constant Field	Value
public static final java.lang.String	CALLABLE_SITES_NAME	"callable"
public static final int	HUGE_FRAGMENT_LENGTH	1000000
public static final int	INDEL_CONTINUATION_QUAL	10
public static final int	INDEL_START_QUAL	30
public static final double	MAX_ALT_FRACTION_IN_NORMAL	0.3
public static final int	MAX_NORMAL_QUAL_SUM	100
public static final int	MIN_PALINDROME_SIZE	5
public static final int	MINIMUM_BASE_QUALITY	6
public static final java.lang.String	NORMAL_SAMPLE_KEY_IN_VCF_HEADER	"normal_sample"
public static final java.lang.String	TUMOR_SAMPLE_KEY_IN_VCF_HEADER	"tumor_sample"

org.broadinstitute.hellbender.tools.walkers.mutect.SomaticLikelihoodsEngine

Modifier and Type	Constant Field	Value
public static final double	CONVERGENCE_THRESHOLD	0.001

org.broadinstitute.hellbender.tools.walkers.mutect.clustering.SomaticClusteringModel

Modifier and Type	Constant Field	Value
public static final double	MAX_FRACTION_OF_BACKGROUND_TO_SPLIT_OFF	0.9

org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls

Modifier and Type	Constant Field	Value
public static final java.lang.String	FILTERING_STATS_EXTENSION	".filteringStats.tsv"
public static final java.lang.String	FILTERING_STATS_LONG_NAME	"filtering-stats"
public static final java.lang.String	FILTERING_STATUS_VCF_KEY	"filtering_status"

org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterStats

Modifier and Type	Constant Field	Value
public static final java.lang.String	FDR_METADATA_TAG	"fdr"
public static final java.lang.String	SENSITIVITY_METADATA_TAG	"sensitivity"
public static final java.lang.String	THRESHOLD_METADATA_TAG	"threshold"

org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection

Modifier and Type	Constant Field	Value
public static final java.lang.String	ARTIFACT_PRIOR_TABLE_NAME	"orientation-bias-artifact-priors"
public static final java.lang.String	ARTIFACT_PRIOR_TABLE_SHORT_NAME	"ob-priors"
public static final java.lang.String	CONTAMINATION_ESTIMATE_LONG_NAME	"contamination-estimate"
public static final java.lang.String	CONTAMINATION_TABLE_LONG_NAME	"contamination-table"
public static final java.lang.String	F_SCORE_BETA_LONG_NAME	"f-score-beta"
public static final java.lang.String	FALSE_DISCOVERY_RATE_LONG_NAME	"false-discovery-rate"
public static final java.lang.String	INITIAL_THRESHOLD_LONG_NAME	"initial-threshold"
public static final java.lang.String	LOG_ARTIFACT_VERSUS_VARIANT_PRIOR_LONG_NAME	"log-artifact-prior"
public static final java.lang.String	LOG_INDEL_PRIOR_LONG_NAME	"log-indel-prior"
public static final java.lang.String	LOG_SNV_PRIOR_LONG_NAME	"log-snv-prior"
public static final java.lang.String	LONG_INDEL_LENGTH_LONG_NAME	"long-indel-length"
public static final java.lang.String	MAX_ALT_ALLELE_COUNT_LONG_NAME	"max-alt-allele-count"
public static final java.lang.String	MAX_DISTANCE_TO_FILTERED_CALL_ON_SAME_HAPLOTYPE_LONG_NAME	"distance-on-haplotype"
public static final java.lang.String	MAX_EVENTS_IN_REGION_LONG_NAME	"max-events-in-region"
public static final java.lang.String	MAX_MEDIAN_FRAGMENT_LENGTH_DIFFERENCE_LONG_NAME	"max-median-fragment-length-difference"
public static final java.lang.String	MAX_N_RATIO_LONG_NAME	"max-n-ratio"
public static final java.lang.String	MIN_AF_LONG_NAME	"min-allele-fraction"
public static final java.lang.String	MIN_MEDIAN_BASE_QUALITY_LONG_NAME	"min-median-base-quality"
public static final java.lang.String	MIN_MEDIAN_MAPPING_QUALITY_LONG_NAME	"min-median-mapping-quality"
public static final java.lang.String	MIN_MEDIAN_READ_POSITION_LONG_NAME	"min-median-read-position"
public static final java.lang.String	MIN_POLYMERASE_SLIPPAGE_LENGTH	"min-slippage-length"
public static final java.lang.String	MIN_READS_ON_EACH_STRAND_LONG_NAME	"min-reads-per-strand"
public static final java.lang.String	NORMAL_P_VALUE_THRESHOLD_LONG_NAME	"normal-p-value-threshold"
public static final java.lang.String	PCR_SLIPPAGE_RATE_LONG_NAME	"pcr-slippage-rate"
public static final java.lang.String	THRESHOLD_STRATEGY_LONG_NAME	"threshold-strategy"
public static final java.lang.String	TUMOR_SEGMENTATION_LONG_NAME	"tumor-segmentation"
public static final java.lang.String	UNIQUE_ALT_READ_COUNT_LONG_NAME	"unique-alt-read-count"

org.broadinstitute.hellbender.tools.walkers.mutect.filtering.MTLowHeteroplasmyFilterTool

Modifier and Type	Constant Field	Value
public static final java.lang.String	LOW_HET_THRESHOLD_LONG_NAME	"low-het-threshold"
public static final java.lang.String	MAX_ALLOWED_LOW_HETS_LONG_NAME	"max-allowed-low-hets"

org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2FilteringEngine

Modifier and Type	Constant Field	Value
public static final double	EPSILON	1.0E-10
public static final double	MIN_REPORTABLE_ERROR_PROBABILITY	0.1

org.broadinstitute.hellbender.tools.walkers.mutect.filtering.NuMTFilterTool

Modifier and Type	Constant Field	Value
public static final java.lang.String	MAX_NUMT_COPIES_IN_AUTOSOME_LONG_NAME	"max-numt-autosomal-copies"
public static final java.lang.String	MEDIAN_AUTOSOMAL_COVERAGE_LONG_NAME	"autosomal-coverage"

org.broadinstitute.hellbender.tools.walkers.readorientation.CollectF1R2CountsArgumentCollection

Modifier and Type	Constant Field	Value
public static final java.lang.String	MAX_DEPTH_LONG_NAME	"f1r2-max-depth"
public static final java.lang.String	MIN_BASE_QUALITY_LONG_NAME	"f1r2-min-bq"
public static final java.lang.String	MIN_MEDIAN_MQ_LONG_NAME	"f1r2-median-mq"

org.broadinstitute.hellbender.tools.walkers.readorientation.F1R2CountsCollector

Modifier and Type	Constant Field	Value
public static final java.lang.String	ALT_HIST_EXTENSION	".alt_histogram"
public static final java.lang.String	ALT_TABLE_EXTENSION	".alt_table"
public static final java.lang.String	REF_HIST_EXTENSION	".ref_histogram"

org.broadinstitute.hellbender.tools.walkers.readorientation.F1R2FilterConstants

Modifier and Type	Constant Field	Value
public static final int	REF_CONTEXT_PADDING	1

org.broadinstitute.hellbender.tools.walkers.readorientation.LearnReadOrientationModel

Modifier and Type	Constant Field	Value
public static final java.lang.String	ARTIFACT_PRIOR_EXTENSION	".orientation_priors"
public static final double	DEFAULT_CONVERGENCE_THRESHOLD	1.0E-4
public static final int	DEFAULT_MAX_ITERATIONS	20
public static final java.lang.String	EM_CONVERGENCE_THRESHOLD_LONG_NAME	"convergence-threshold"
public static final java.lang.String	MAX_DEPTH_LONG_NAME	"max-depth"
public static final java.lang.String	MAX_EM_ITERATIONS_LONG_NAME	"num-em-iterations"

org.broadinstitute.hellbender.tools.walkers.realignmentfilter.FilterAlignmentArtifacts

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_DISTANCE_TO_GROUP_VARIANTS	1000
public static final int	DEFAULT_INDEL_START_TOLERANCE	5
public static final int	DEFAULT_KMER_SIZE	21
public static final int	DEFAULT_MAX_GROUPED_SPAN	10000
public static final int	DEFAULT_REF_PADDING	100
public static final java.lang.String	DONT_SKIP_ALREADY_FILTERED_VARIANTS_LONG_NAME	"dont-skip-filtered-variants"
public static final java.lang.String	INDEL_START_TOLERANCE_LONG_NAME	"indel-start-tolerance"
public static final java.lang.String	KMER_SIZE_LONG_NAME	"kmer-size"

org.broadinstitute.hellbender.tools.walkers.realignmentfilter.RealignmentArgumentCollection

Modifier and Type	Constant Field	Value
public static final double	DEFAULT_DROP_RATIO	0.2
public static final int	DEFAULT_MAX_REASONABLE_FRAGMENT_LENGTH	100000
public static final double	DEFAULT_MIN_ALIGNER_SCORE_DIFFERENCE_PER_BASE	0.2
public static final double	DEFAULT_MIN_MISMATCH_DIFFERENCE_PER_BASE	0.02
public static final int	DEFAULT_MIN_SEED_LENGTH	14
public static final int	DEFAULT_NUM_REGULAR_CONTIGS	250000
public static final double	DEFAULT_SEED_SPLIT_FACTOR	0.5

org.broadinstitute.hellbender.tools.walkers.rnaseq.OverhangFixingManager

Modifier and Type	Constant Field	Value
protected static final int	MAX_SPLICES_TO_KEEP	1000

org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence

Modifier and Type	Constant Field	Value
public static final java.lang.String	ALLELE_COUNT_INPUT_ARGUMENT_LONG_NAME	"allele-count-vcf"
public static final java.lang.String	ALLELE_COUNT_INPUT_ARGUMENT_SHORT_NAME	"F"
public static final java.lang.String	ALLELE_COUNT_OUTPUT_ARGUMENT_LONG_NAME	"allele-count-file"
public static final java.lang.String	ALLELE_COUNT_OUTPUT_ARGUMENT_SHORT_NAME	"AC"
public static final java.lang.String	COMPRESSION_LEVEL_ARGUMENT_LONG_NAME	"compression-level"
public static final java.lang.String	PAIRED_END_FILE_ARGUMENT_LONG_NAME	"pe-file"
public static final java.lang.String	PAIRED_END_FILE_ARGUMENT_SHORT_NAME	"PE"
public static final java.lang.String	SAMPLE_NAME_ARGUMENT_LONG_NAME	"sample-name"
public static final java.lang.String	SPLIT_READ_FILE_ARGUMENT_LONG_NAME	"sr-file"
public static final java.lang.String	SPLIT_READ_FILE_ARGUMENT_SHORT_NAME	"SR"

org.broadinstitute.hellbender.tools.walkers.sv.JointGermlineCNVSegmentation

Modifier and Type	Constant Field	Value
public static final java.lang.String	ALT_ALLELE_SUMMARY_STRATEGY_LONG_NAME	"alt-allele-summary-strategy"
public static final java.lang.String	BREAKPOINT_SUMMARY_STRATEGY_LONG_NAME	"breakpoint-summary-strategy"
public static final java.lang.String	CLUSTERING_BREAKEND_WINDOW_LONG_NAME	"clustering-breakend-window"
public static final java.lang.String	CLUSTERING_INTERVAL_OVERLAP_LONG_NAME	"clustering-interval-overlap"
public static final java.lang.String	DEFRAGMENTATION_PADDING_LONG_NAME	"defragmentation-padding-fraction"
public static final java.lang.String	MIN_QUALITY_LONG_NAME	"minimum-qs-score"
public static final java.lang.String	MIN_SAMPLE_NUM_OVERLAP_LONG_NAME	"min-sample-set-fraction-overlap"
public static final java.lang.String	MODEL_CALL_INTERVALS_LONG_NAME	"model-call-intervals"

org.broadinstitute.hellbender.tools.walkers.validation.AnnotateVcfWithBamDepth

Modifier and Type	Constant Field	Value
public static final java.lang.String	POOLED_BAM_DEPTH_ANNOTATION_NAME	"BAM_DEPTH"

org.broadinstitute.hellbender.tools.walkers.validation.AnnotateVcfWithExpectedAlleleFraction

Modifier and Type	Constant Field	Value
public static final java.lang.String	EXPECTED_ALLELE_FRACTION_NAME	"AF_EXP"
public static final java.lang.String	MIXING_FRACTIONS_TABLE_NAME	"mixing-fractions"

org.broadinstitute.hellbender.tools.walkers.validation.Concordance

Modifier and Type	Constant Field	Value
public static final java.lang.String	FILTER_ANALYSIS_LONG_NAME	"filter-analysis"
public static final java.lang.String	FILTERED_TRUE_NEGATIVES_AND_FALSE_NEGATIVES_LONG_NAME	"filtered-true-negatives-and-false-negatives"
public static final java.lang.String	FILTERED_TRUE_NEGATIVES_AND_FALSE_NEGATIVES_SHORT_NAME	"ftnfn"
public static final java.lang.String	SUMMARY_LONG_NAME	"summary"
public static final java.lang.String	SUMMARY_SHORT_NAME	"S"
public static final java.lang.String	TRUE_POSITIVES_AND_FALSE_NEGATIVES_LONG_NAME	"true-positives-and-false-negatives"
public static final java.lang.String	TRUE_POSITIVES_AND_FALSE_NEGATIVES_SHORT_NAME	"tpfn"
public static final java.lang.String	TRUE_POSITIVES_AND_FALSE_POSITIVES_LONG_NAME	"true-positives-and-false-positives"
public static final java.lang.String	TRUE_POSITIVES_AND_FALSE_POSITIVES_SHORT_NAME	"tpfp"
public static final java.lang.String	TRUTH_STATUS_VCF_ATTRIBUTE	"STATUS"

org.broadinstitute.hellbender.tools.walkers.validation.EvaluateInfoFieldConcordance

Modifier and Type	Constant Field	Value
public static final java.lang.String	SUMMARY_LONG_NAME	"summary"
public static final java.lang.String	SUMMARY_SHORT_NAME	"S"

org.broadinstitute.hellbender.tools.walkers.validation.FalsePositiveRecord

Modifier and Type	Constant Field	Value
public static final java.lang.String	ID_COLUMN_NAME	"id"
public static final java.lang.String	INDEL_COLUMN_NAME	"indel"
public static final java.lang.String	INDEL_FPR_COLUMN_NAME	"indel_FPR"
public static final java.lang.String	SNP_COLUMN_NAME	"snp"
public static final java.lang.String	SNP_FPR_COLUMN_NAME	"snp_FPR"
public static final java.lang.String	TARGET_TERRITORY_COLUMN_NAME	"target_territory"

org.broadinstitute.hellbender.tools.walkers.validation.MergeMutect2CallsWithMC3

Modifier and Type	Constant Field	Value
public static final java.lang.String	CENTERS_KEY	"CENTERS"
public static final java.lang.String	M2_CENTER_NAME	"M2"
public static final java.lang.String	M2_FILTERS_KEY	"M2_FILTERS"
public static final java.lang.String	MC3_ALT_COUNT_KEY	"NALT"
public static final java.lang.String	MC3_REF_COUNT_KEY	"NREF"

org.broadinstitute.hellbender.tools.walkers.validation.ReferenceBlockConcordance

Modifier and Type	Constant Field	Value
public static final java.lang.String	CONFIDENCE_CONCORDANCE_HISTOGRAM_LONG_NAME	"confidence-concordance-histogram"
public static final java.lang.String	CONFIDENCE_CONCORDANCE_HISTOGRAM_SHORT_NAME	"cch"
public static final java.lang.String	EVAL_BLOCK_HISTOGRAM_LONG_NAME	"eval-block-histogram"
public static final java.lang.String	EVAL_BLOCK_HISTOGRAM_SHORT_NAME	"ebh"
public static final java.lang.String	TRUTH_BLOCK_HISTOGRAM_LONG_NAME	"truth-block-histogram"
public static final java.lang.String	TRUTH_BLOCK_HISTOGRAM_SHORT_NAME	"tbh"

org.broadinstitute.hellbender.tools.walkers.validation.RemoveNearbyIndels

Modifier and Type	Constant Field	Value
public static final java.lang.String	MIN_INDEL_SPACING_NAME	"min-indel-spacing"

org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.PowerCalculationUtils

Modifier and Type	Constant Field	Value
public static final int	MINIMUM_NUM_READS_FOR_SIGNAL_COUNT	2
public static final double	P_VALUE_FOR_NOISE	0.99

org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations

Modifier and Type	Constant Field	Value
public static final java.lang.String	ANNOTATED_VCF_LONG_NAME	"annotated-vcf"
public static final java.lang.String	CUTOFF_LONG_NAME	"min-base-quality-cutoff"
public static final int	DEFAULT_MIN_BQ_CUTOFF	20
public static final java.lang.String	JUDGMENT_INFO_FIELD_KEY	"JUDGMENT"
public static final java.lang.String	MAX_VALIDATION_NORMAL_COUNT_LONG_NAME	"max-validation-normal-count"
public static final java.lang.String	MIN_POWER_LONG_NAME	"min-power"
public static final java.lang.String	POWER_INFO_FIELD_KEY	"POWER"
public static final java.lang.String	SAMPLE_NAME_DISCOVERY_VCF_LONG_NAME	"discovery-sample-name"
public static final java.lang.String	SAMPLE_NAME_VALIDATION_CASE	"val-case-sample-name"
public static final java.lang.String	SAMPLE_NAME_VALIDATION_CONTROL	"val-control-sample-name"
public static final java.lang.String	VALIDATION_AD_INFO_FIELD_KEY	"VAL_AD"

org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection

Modifier and Type	Constant Field	Value
public static final java.lang.String	ALL_FAMILY_NAME	"all"
public static final java.lang.String	ALL_SAMPLE_NAME	"all"

org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalEngine

Modifier and Type	Constant Field	Value
public static final java.lang.String	IS_SINGLETON_KEY	"ISSINGLETON"

org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.IndelLengthHistogram

Modifier and Type	Constant Field	Value
public static final int	MAX_SIZE_FOR_HISTOGRAM	10

org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.IndelSummary

Modifier and Type	Constant Field	Value
public static final int	LARGE_INDEL_SIZE_THRESHOLD	10

org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.SnpEffPositionModifier

Modifier and Type	Constant Field	Value
public static final java.lang.String	EFFECT_KEY	"SNPEFF_EFFECT"

org.broadinstitute.hellbender.tools.walkers.variantutils.CalculateGenotypePosteriors

Modifier and Type	Constant Field	Value
public static final java.lang.String	NUM_REF_SAMPLES_LONG_NAME	"num-reference-samples-if-no-call"
public static final java.lang.String	SUPPORTING_CALLSETS_LONG_NAME	"supporting-callsets"
public static final java.lang.String	SUPPORTING_CALLSETS_SHORT_NAME	"supporting"

org.broadinstitute.hellbender.tools.walkers.variantutils.FamilyLikelihoods

Modifier and Type	Constant Field	Value
public final double	NO_JOINT_VALUE	-1.0

org.broadinstitute.hellbender.tools.walkers.variantutils.LeftAlignAndTrimVariants

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_MAX_LEADING_BASES	1000
public static final java.lang.String	DONT_TRIM_ALLELES_LONG_NAME	"dont-trim-alleles"
public static final java.lang.String	DONT_TRIM_ALLELES_SHORT_NAME	"no-trim"
public static final java.lang.String	KEEP_ORIGINAL_AC_LONG_NAME	"keep-original-ac"
public static final java.lang.String	MAX_INDEL_LENGTH_LONG_NAME	"max-indel-length"
public static final java.lang.String	MAX_LEADING_BASES_LONG_NAME	"max-leading-bases"
public static final java.lang.String	SPLIT_MULTIALLELEICS_LONG_NAME	"split-multi-allelics"

org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF

Modifier and Type	Constant Field	Value
public static final java.lang.String	ALLOW_MISSING_LONG_NAME	"allow-missing-hom-ref-data"
public static final java.lang.String	DROP_LOW_QUALS_ARG_NAME	"drop-low-quals"
public static final java.lang.String	KEEP_ALL_ALTS_ARG_NAME	"keep-all-alts"
public static final java.lang.String	QUAL_APPROX_LONG_NAME	"do-qual-score-approximation"
public static final java.lang.String	QUAL_APPROX_SHORT_NAME	"do-qual-approx"
public static final java.lang.String	RGQ_THRESHOLD_LONG_NAME	"rgq-threshold-to-no-call"
public static final java.lang.String	RGQ_THRESHOLD_SHORT_NAME	"rgq-threshold"

org.broadinstitute.hellbender.tools.walkers.variantutils.UpdateVCFSequenceDictionary

Modifier and Type	Constant Field	Value
public static final java.lang.String	DICTIONARY_ARGUMENT_NAME	"source-dictionary"
public static final java.lang.String	REPLACE_ARGUMENT_NAME	"replace"

org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants

Modifier and Type	Constant Field	Value
public static final java.lang.String	DO_NOT_VALIDATE_FILTERED_RECORDS	"do-not-validate-filtered-records"
public static final java.lang.String	GVCF_VALIDATE	"validate-GVCF"

org.broadinstitute.hellbender.tools.walkers.variantutils.VariantsToTable

Modifier and Type	Constant Field	Value
public static final java.lang.String	SPLIT_MULTI_ALLELIC_LONG_NAME	"split-multi-allelic"
public static final java.lang.String	SPLIT_MULTI_ALLELIC_SHORT_NAME	"SMA"

org.broadinstitute.hellbender.tools.walkers.vqsr.ApplyVQSR

Modifier and Type	Constant Field	Value
protected static final java.lang.String	LOW_VQSLOD_FILTER_NAME	"LOW_VQSLOD"

org.broadinstitute.hellbender.tools.walkers.vqsr.Tranche

Modifier and Type	Constant Field	Value
protected static final java.lang.String	COMMENT_STRING	"#"
protected static final java.lang.String	DEFAULT_TRANCHE_NAME	"anonymous"
protected static final int	EXPECTED_COLUMN_COUNT	11
protected static final java.lang.String	VALUE_SEPARATOR	","

org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibratorEngine

Modifier and Type	Constant Field	Value
public static final double	MIN_ACCEPTABLE_LOD_SCORE	-20000.0

org.broadinstitute.hellbender.transformers.DUSTReadTransformer

Modifier and Type	Constant Field	Value
public static final long	serialVersionUID	1L

org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer

Modifier and Type	Constant Field	Value
public static final double	MIN_FRACTION_OF_MATCHING_BASES	0.9

org.broadinstitute.hellbender.transformers.ReadTransformer

Modifier and Type	Constant Field	Value
public static final long	serialVersionUID	1L

org.broadinstitute.hellbender.transformers.StripMateNumberTransformer

Modifier and Type	Constant Field	Value
public static final long	serialVersionUID	1L

org.broadinstitute.hellbender.transformers.VariantTransformer

Modifier and Type	Constant Field	Value
public static final long	serialVersionUID	1L

org.broadinstitute.hellbender.utils.GenomeLocParser

Modifier and Type	Constant Field	Value
public static final java.lang.String	UNMAPPED_LOC_NAME	"unmapped"

org.broadinstitute.hellbender.utils.IntervalPileup

Modifier and Type	Constant Field	Value
public static final byte	GAP	45
public static final byte	NO_BASE	-1
public static final byte	NO_BQ	-1

org.broadinstitute.hellbender.utils.MathUtils

Modifier and Type	Constant Field	Value
public static final double	LOG10_P_OF_ZERO	-1000000.0

org.broadinstitute.hellbender.utils.QualityUtils

Modifier and Type	Constant Field	Value
public static final int	MAPPING_QUALITY_UNAVAILABLE	255
public static final int	MAX_QUAL	254
public static final byte	MAX_REASONABLE_Q_SCORE	60
public static final byte	MAX_SAM_QUAL_SCORE	93
public static final byte	MIN_USABLE_Q_SCORE	6

org.broadinstitute.hellbender.utils.SimpleInterval

Modifier and Type	Constant Field	Value
public static final char	CONTIG_SEPARATOR	58
public static final java.lang.String	END_OF_CONTIG	"+"
public static final char	START_END_SEPARATOR	45

org.broadinstitute.hellbender.utils.Utils

Modifier and Type	Constant Field	Value
public static final float	JAVA_DEFAULT_HASH_LOAD_FACTOR	0.75f

org.broadinstitute.hellbender.utils.activityprofile.BandPassActivityProfile

Modifier and Type	Constant Field	Value
public static final double	DEFAULT_SIGMA	17.0
public static final int	MAX_FILTER_SIZE	50

org.broadinstitute.hellbender.utils.baq.BAQ

Modifier and Type	Constant Field	Value
public static final java.lang.String	BAQ_TAG	"BQ"
public static final int	DEFAULT_BANDWIDTH	7
public static final double	DEFAULT_GOP	40.0

org.broadinstitute.hellbender.utils.codecs.AnnotatedIntervalCodec

Modifier and Type	Constant Field	Value
public static final java.lang.String	ANNOTATED_INTERVAL_DEFAULT_CONFIG_RESOURCE	"org/broadinstitute/hellbender/tools/copynumber/utils/annotatedinterval/annotated_region_default.config"
public static final java.lang.String	CONTIG_COL_COMMENT	"_ContigHeader="
public static final java.lang.String	END_COL_COMMENT	"_EndHeader="
public static final java.lang.String	START_COL_COMMENT	"_StartHeader="

org.broadinstitute.hellbender.utils.codecs.BafEvidenceCodec

Modifier and Type	Constant Field	Value
public static final java.lang.String	COL_DELIMITER	"\t"
public static final java.lang.String	FORMAT_SUFFIX	".baf.txt"

org.broadinstitute.hellbender.utils.codecs.DepthEvidenceCodec

Modifier and Type	Constant Field	Value
public static final java.lang.String	COL_DELIMITER	"\t"
public static final java.lang.String	FORMAT_SUFFIX	".rd.txt"

org.broadinstitute.hellbender.utils.codecs.DiscordantPairEvidenceCodec

Modifier and Type	Constant Field	Value
public static final java.lang.String	COL_DELIMITER	"\t"
public static final java.lang.String	FORMAT_SUFFIX	".pe.txt"
public static final java.lang.String	STRAND_MINUS	"-"
public static final java.lang.String	STRAND_PLUS	"+"

org.broadinstitute.hellbender.utils.codecs.LocusDepthCodec

Modifier and Type	Constant Field	Value
public static final java.lang.String	FORMAT_SUFFIX	".ld.txt"

org.broadinstitute.hellbender.utils.codecs.SplitReadEvidenceCodec

Modifier and Type	Constant Field	Value
public static final java.lang.String	COL_DELIMITER	"\t"
public static final java.lang.String	DIRECTION_LEFT	"left"
public static final java.lang.String	DIRECTION_RIGHT	"right"
public static final java.lang.String	FORMAT_SUFFIX	".sr.txt"

org.broadinstitute.hellbender.utils.codecs.gtf.AbstractGtfCodec

Modifier and Type	Constant Field	Value
public static final java.lang.String	GTF_FILE_EXTENSION	"gtf"

org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfCodec

Modifier and Type	Constant Field	Value
public static final java.lang.String	GENCODE_GTF_FILE_PREFIX	"gencode"
public static final java.lang.String	GTF_FILE_TYPE_STRING	"GENCODE"

org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature

Modifier and Type	Constant Field	Value
public static final java.lang.String	ANNOTATION_SOURCE_ENA	"ena"
public static final java.lang.String	ANNOTATION_SOURCE_ENSEMBL	"ENSEMBL"
public static final java.lang.String	ANNOTATION_SOURCE_HAVANA	"HAVANA"
public static final java.lang.String	EXTRA_FIELD_KEY_VALUE_SPLITTER	" "
public static final int	NO_EXON_NUMBER	-1
public static final int	NO_FEATURE_ORDER	-1

org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqCodec

Modifier and Type	Constant Field	Value
public static final int	CODING_START_INDEX	6
public static final int	CODING_STOP_INDEX	7
public static final java.lang.String	COMMENT_LINE_CHARACTER	"#"
public static final int	CONTIG_INDEX	2
public static final int	EXON_FRAMES_INDEX	15
public static final int	EXON_STARTS_INDEX	9
public static final int	EXON_STOPS_INDEX	10
protected static final java.lang.String	FILE_EXT	"refseq"
public static final int	GENE_NAME_INDEX	12
public static final int	INTERVAL_LEFT_BOUND_INDEX	4
public static final int	INTERVAL_RIGHT_BOUND_INDEX	5
public static final java.lang.String	LINE_DELIMITER	"\t"
public static final int	MINIMUM_LINE_FIELD_COUNT	16
public static final int	STRAND_INDEX	3
public static final int	TRANSCRIPT_ID_INDEX	1

org.broadinstitute.hellbender.utils.codecs.table.TableCodec

Modifier and Type	Constant Field	Value
protected static final java.lang.String	COMMENT_DELIMITER	"#"
protected static final java.lang.String	DEFAULT_HEADER_DELIMITER	"HEADER"
protected static final java.lang.String	IGV_HEADER_DELIMITER	"track"

org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable.XsvLocatableTableCodec

Modifier and Type	Constant Field	Value
public static final java.lang.String	CONFIG_FILE_EXTENSION	".config"
public static final java.lang.String	SAM_FILE_HEADER_LINE_START	"@"
public static final java.lang.String	SAM_FILE_HEADER_START	"@HD\tVN:"

org.broadinstitute.hellbender.utils.collections.HopscotchCollection<T>

Modifier and Type	Constant Field	Value
protected static final double	LOAD_FACTOR	0.85
protected static final int	SPREADER	241

org.broadinstitute.hellbender.utils.config.GATKConfig

Modifier and Type	Constant Field	Value
public static final java.lang.String	CONFIG_FILE_VARIABLE_CLASS_PATH	"GATKConfig.classPathToGatkConfig"
public static final java.lang.String	CONFIG_FILE_VARIABLE_FILE_NAME	"GATKConfig.pathToGatkConfig"
public static final java.lang.String	DEFAULT_ANNOTATION_PACKAGES	"org.broadinstitute.hellbender.tools.walkers.annotator"

org.broadinstitute.hellbender.utils.dragstr.DragstrParamUtils

Modifier and Type	Constant Field	Value
public static final java.lang.String	API_TABLE_NAME	"API"
public static final java.lang.String	GCP_TABLE_NAME	"GCP"
public static final java.lang.String	GOP_TABLE_NAME	"GOP"

org.broadinstitute.hellbender.utils.dragstr.STRTableFile

Modifier and Type	Constant Field	Value
public static final java.lang.String	DECIMATION_TABLE_FILE_NAME	"decimation.txt"
public static final java.lang.String	REF_DICTIONARY_FILE_NAME	"reference.dict"
public static final java.lang.String	SITES_FILE_NAME	"sites.bin"
public static final java.lang.String	SITES_INDEX_FILE_NAME	"sites.idx"
public static final java.lang.String	SITES_TEXT_FILE_NAME	"sites.txt"
public static final java.lang.String	SUMMARY_FILE_NAME	"summary.txt"

org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile

Modifier and Type	Constant Field	Value
public static final long	DEFAULT_CACHE_SIZE	1000000L

org.broadinstitute.hellbender.utils.fragments.FragmentUtils

Modifier and Type	Constant Field	Value
public static final double	DEFAULT_PCR_SNV_ERROR_RATE	1.0E-4

org.broadinstitute.hellbender.utils.gcs.BucketUtils

Modifier and Type	Constant Field	Value
public static final java.lang.String	FILE_PREFIX	"file:"
public static final java.lang.String	GCS_PREFIX	"gs://"
public static final java.lang.String	HDFS_PREFIX	"hdfs://"
public static final java.lang.String	HDFS_SCHEME	"hdfs"
public static final java.lang.String	HTTP_PREFIX	"http://"
public static final java.lang.String	HTTPS_PREFIX	"https://"

org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods<EVIDENCE extends htsjdk.samtools.util.Locatable,A extends htsjdk.variant.variantcontext.Allele>

Modifier and Type	Constant Field	Value
public static final double	LOG_10_INFORMATIVE_THRESHOLD	0.2

org.broadinstitute.hellbender.utils.haplotype.EventMap

Modifier and Type	Constant Field	Value
protected static final int	MIN_NUMBER_OF_EVENTS_TO_COMBINE_INTO_BLOCK_SUBSTITUTION	3

org.broadinstitute.hellbender.utils.haplotype.HaplotypeBAMWriter

Modifier and Type	Constant Field	Value
public static final java.lang.String	DEFAULT_GATK3_HAPLOTYPE_READ_GROUP_ID	"ArtificialHaplotype"
public static final java.lang.String	DEFAULT_HAPLOTYPE_READ_GROUP_ID	"ArtificialHaplotypeRG"

org.broadinstitute.hellbender.utils.help.GATKWDLDoclet

Modifier and Type	Constant Field	Value
public static final java.lang.String	OPT_BUILD_DIR	"-build-dir"

org.broadinstitute.hellbender.utils.help.HelpConstants

Modifier and Type	Constant Field	Value
public static final java.lang.String	DOC_CAT_ANNOTATORS	"Variant Annotations"
public static final java.lang.String	DOC_CAT_ANNOTATORS_SUMMARY	"Available to HaplotypeCaller, Mutect2, VariantAnnotator and GenotypeGVCFs. See https://software.broadinstitute.org/gatk/documentation/article?id=10836"
public static final java.lang.String	DOC_CAT_CNV	"Copy Number Variant Discovery"
public static final java.lang.String	DOC_CAT_CNV_SUMMARY	"Tools that analyze read coverage to detect copy number variants."
public static final java.lang.String	DOC_CAT_COVERAGE_ANALYSIS	"Coverage Analysis"
public static final java.lang.String	DOC_CAT_COVERAGE_ANALYSIS_SUMMARY	"Tools that count coverage, e.g. depth per allele"
public static final java.lang.String	DOC_CAT_EXAMPLE	"Example Tools"
public static final java.lang.String	DOC_CAT_EXAMPLE_SUMMARY	"Example tools that show developers how to implement new tools"
public static final java.lang.String	DOC_CAT_METAGENOMICS	"Metagenomics"
public static final java.lang.String	DOC_CAT_METAGENOMICS_SUMMARY	"Tools that perform metagenomic analysis, e.g. microbial community composition and pathogen detection"
public static final java.lang.String	DOC_CAT_METHYLATION_DISCOVERY	"Methylation-Specific Tools"
public static final java.lang.String	DOC_CAT_METHYLATION_DISCOVERY_SUMMARY	"Tools that perform methylation calling, processing bisulfite sequenced, methylation-aware aligned BAM"
public static final java.lang.String	DOC_CAT_READFILTERS	"Read Filters"
public static final java.lang.String	DOC_CAT_READFILTERS_SUMMARY	"Applied by engine to select reads for analysis"
public static final java.lang.String	DOC_CAT_RNA	"RNA-Specific Tools"
public static final java.lang.String	DOC_CAT_RNA_SUMMARY	"Tools intended to be used for processing RNA data."
public static final java.lang.String	DOC_CAT_SHORT_VARIANT_DISCOVERY	"Short Variant Discovery"
public static final java.lang.String	DOC_CAT_SHORT_VARIANT_DISCOVERY_SUMMARY	"Tools that perform variant calling and genotyping for short variants (SNPs, SNVs and Indels)"
public static final java.lang.String	DOC_CAT_SV_DISCOVERY	"Structural Variant Discovery"
public static final java.lang.String	DOC_CAT_SV_DISCOVERY_SUMMARY	"Tools that detect structural variants"
public static final java.lang.String	DOC_CAT_TEST	"Test Tools"
public static final java.lang.String	DOC_CAT_TEST_SUMMARY	"Tools for internal test purposes"
public static final java.lang.String	GATK_FORUM_URL	"http://gatkforums.broadinstitute.org/"
public static final java.lang.String	GATK_MAIN_SITE	"https://software.broadinstitute.org/gatk/"

org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream

Modifier and Type	Constant Field	Value
public static final java.lang.String	BCI_FILE_EXTENSION	".bci"
public static final int	FILE_POINTER_OFFSET	22

org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream.Writer<F extends htsjdk.tribble.Feature>

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_COMPRESSION_LEVEL	6

org.broadinstitute.hellbender.utils.io.IOUtils

Modifier and Type	Constant Field	Value
public static final java.lang.String	GENOMIC_DB_URI_SCHEME	"gendb"

org.broadinstitute.hellbender.utils.io.Resource

Modifier and Type	Constant Field	Value
public static final java.lang.String	LARGE_RUNTIME_RESOURCES_PATH	"large"

org.broadinstitute.hellbender.utils.logging.BunnyLog

Modifier and Type	Constant Field	Value
public static final java.lang.String	bunny	"=[**]="

org.broadinstitute.hellbender.utils.mcmc.PosteriorSummaryUtils

Modifier and Type	Constant Field	Value
public static final double	SILVERMANS_RULE_CONSTANT	1.06
public static final double	SILVERMANS_RULE_EXPONENT	-0.2

org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter

Modifier and Type	Constant Field	Value
protected static final int	BUFFER_SIZE_BYTES	1048576
protected static final int	COPY_SPEED_HISTORY_SIZE	10
protected static final long	DAY_IN_MS	86400000L
protected static final double	DEFAULT_PROGRESS_DISPLAY_PERCENT_INCREMENT	0.25
protected static final long	HOUR_IN_MS	3600000L
protected static final int	KB_TO_BYTES	1024
protected static final long	MINUTE_IN_MS	60000L
protected static final int	MS_TO_SEC	1000
protected static final int	NANOS_TO_MILLIS	1000000
protected static final int	NANOS_TO_SECONDS	1000000000
protected static final boolean	OVERWRITE_EXISTING_DEFAULT	false
protected static final long	SECOND_IN_MS	1000L

org.broadinstitute.hellbender.utils.pairhmm.PairHMM

Modifier and Type	Constant Field	Value
public static final byte	BASE_QUALITY_SCORE_THRESHOLD	18

org.broadinstitute.hellbender.utils.pairhmm.PairHMMModel

Modifier and Type	Constant Field	Value
public static final int	deletionToDeletion	5
public static final int	indelToMatch	1
public static final int	insertionToInsertion	3
public static final int	matchToDeletion	4
public static final int	matchToInsertion	2
public static final int	matchToMatch	0
public static final int	TRANS_PROB_ARRAY_LENGTH	6

org.broadinstitute.hellbender.utils.pileup.PileupElement

Modifier and Type	Constant Field	Value
public static final byte	A_FOLLOWED_BY_INSERTION_BASE	87
public static final byte	C_FOLLOWED_BY_INSERTION_BASE	88
public static final byte	DELETION_QUAL	16
public static final byte	G_FOLLOWED_BY_INSERTION_BASE	90
public static final byte	T_FOLLOWED_BY_INSERTION_BASE	89

org.broadinstitute.hellbender.utils.pileup.ReadPileup

Modifier and Type	Constant Field	Value
public static final double	SAMTOOLS_OVERLAP_LOW_CONFIDENCE	0.8

org.broadinstitute.hellbender.utils.python.PythonExecutorBase

Modifier and Type	Constant Field	Value
public static final java.lang.String	PYTHON_EXTENSION	".py"

org.broadinstitute.hellbender.utils.R.RScriptLibrary

Modifier and Type	Constant Field	Value
public static final java.lang.String	R_LIBRARY_SUFFIX	".tar.gz"

org.broadinstitute.hellbender.utils.read.AlignmentUtils

Modifier and Type	Constant Field	Value
public static final byte	GAP_CHARACTER	45
public static final java.lang.String	HAPLOTYPE_TAG	"HC"

org.broadinstitute.hellbender.utils.read.ArtificialReadUtils

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_READ_LENGTH	50
public static final java.lang.String	READ_GROUP_ID	"x"

org.broadinstitute.hellbender.utils.read.ReadConstants

Modifier and Type	Constant Field	Value
public static final int	NO_MAPPING_QUALITY	0
public static final java.lang.String	NULL_SEQUENCE_STRING	"*"
public static final java.lang.String	UNSET_CONTIG	"*"
public static final int	UNSET_POSITION	0

org.broadinstitute.hellbender.utils.read.ReadUtils

Modifier and Type	Constant Field	Value
public static final java.lang.String	BQSR_BASE_DELETION_QUALITIES	"BD"
public static final java.lang.String	BQSR_BASE_INSERTION_QUALITIES	"BI"
public static final byte	DEFAULT_INSERTION_DELETION_QUAL	45
public static final int	READ_INDEX_NOT_FOUND	-1
public static final int	SAM_DUPLICATE_READ_FLAG	1024
public static final int	SAM_FIRST_OF_PAIR_FLAG	64
public static final int	SAM_MATE_STRAND_FLAG	32
public static final int	SAM_MATE_UNMAPPED_FLAG	8
public static final int	SAM_NOT_PRIMARY_ALIGNMENT_FLAG	256
public static final int	SAM_PROPER_PAIR_FLAG	2
public static final int	SAM_READ_FAILS_VENDOR_QUALITY_CHECK_FLAG	512
public static final int	SAM_READ_PAIRED_FLAG	1
public static final int	SAM_READ_STRAND_FLAG	16
public static final int	SAM_READ_UNMAPPED_FLAG	4
public static final int	SAM_SECOND_OF_PAIR_FLAG	128
public static final int	SAM_SUPPLEMENTARY_ALIGNMENT_FLAG	2048

org.broadinstitute.hellbender.utils.read.markduplicates.LibraryIdGenerator

Modifier and Type	Constant Field	Value
public static final java.lang.String	UNKNOWN_LIBRARY	"Unknown Library"

org.broadinstitute.hellbender.utils.read.markduplicates.MarkDuplicatesScoringStrategy

Modifier and Type	Constant Field	Value
public static final int	MIN_BASE_QUAL	15

org.broadinstitute.hellbender.utils.read.mergealignment.AbstractAlignmentMerger

Modifier and Type	Constant Field	Value
public static final int	MAX_RECORDS_IN_RAM	500000

org.broadinstitute.hellbender.utils.recalibration.RecalDatum

Modifier and Type	Constant Field	Value
public static final byte	MAX_GATK_USABLE_Q_SCORE	40
public static final byte	MAX_RECALIBRATED_Q_SCORE	93

org.broadinstitute.hellbender.utils.recalibration.RecalibrationArgumentCollection

Modifier and Type	Constant Field	Value
public static final boolean	DO_NOT_USE_STANDARD_COVARIATES	false
public static final boolean	RUN_WITHOUT_DBSNP	false
public static final java.lang.String	SOLID_NOCALL_STRATEGY	"THROW_EXCEPTION"
public static final java.lang.String	SOLID_RECAL_MODE	"SET_Q_ZERO"

org.broadinstitute.hellbender.utils.recalibration.RecalUtils

Modifier and Type	Constant Field	Value
public static final java.lang.String	ALL_COVARIATES_REPORT_TABLE_TITLE	"RecalTable2"
public static final java.lang.String	ARGUMENT_COLUMN_NAME	"Argument"
public static final java.lang.String	ARGUMENT_REPORT_TABLE_TITLE	"Arguments"
public static final java.lang.String	ARGUMENT_VALUE_COLUMN_NAME	"Value"
public static final java.lang.String	COVARIATE_NAME_COLUMN_NAME	"CovariateName"
public static final java.lang.String	COVARIATE_VALUE_COLUMN_NAME	"CovariateValue"
public static final int	EMPIRICAL_Q_REPORTED_DECIMAL_PLACES	4
public static final int	EMPIRICAL_QUAL_DECIMAL_PLACES	4
public static final java.lang.String	EMPIRICAL_QUALITY_COLUMN_NAME	"EmpiricalQuality"
public static final java.lang.String	ESTIMATED_Q_REPORTED_COLUMN_NAME	"EstimatedQReported"
public static final java.lang.String	EVENT_TYPE_COLUMN_NAME	"EventType"
public static final java.lang.String	NUMBER_ERRORS_COLUMN_NAME	"Errors"
public static final int	NUMBER_ERRORS_DECIMAL_PLACES	2
public static final java.lang.String	NUMBER_OBSERVATIONS_COLUMN_NAME	"Observations"
public static final java.lang.String	QUALITY_SCORE_COLUMN_NAME	"QualityScore"
public static final java.lang.String	QUALITY_SCORE_REPORT_TABLE_TITLE	"RecalTable1"
public static final java.lang.String	QUANTIZED_COUNT_COLUMN_NAME	"Count"
public static final java.lang.String	QUANTIZED_REPORT_TABLE_TITLE	"Quantized"
public static final java.lang.String	QUANTIZED_VALUE_COLUMN_NAME	"QuantizedScore"
public static final java.lang.String	READGROUP_COLUMN_NAME	"ReadGroup"
public static final java.lang.String	READGROUP_REPORT_TABLE_TITLE	"RecalTable0"

org.broadinstitute.hellbender.utils.recalibration.covariates.Covariate

Modifier and Type	Constant Field	Value
public static final long	serialVersionUID	1L

org.broadinstitute.hellbender.utils.recalibration.covariates.CycleCovariate

Modifier and Type	Constant Field	Value
public static final int	CUSHION_FOR_INDELS	4

org.broadinstitute.hellbender.utils.report.GATKReport

Modifier and Type	Constant Field	Value
public static final java.lang.String	GATKREPORT_HEADER_PREFIX	"#:GATKReport."
public static final java.lang.String	RECAL_FILE	"input covariates table file for base quality score recalibration"

org.broadinstitute.hellbender.utils.report.GATKReportTable

Modifier and Type	Constant Field	Value
public static final java.lang.String	INVALID_TABLE_NAME_REGEX	"[^a-zA-Z0-9_\\-\\.]"

org.broadinstitute.hellbender.utils.runtime.CapturedStreamOutput

Modifier and Type	Constant Field	Value
public static final int	STREAM_BLOCK_TRANSFER_SIZE	4096

org.broadinstitute.hellbender.utils.tsv.DataLine

Modifier and Type	Constant Field	Value
public static final long	NO_LINE_NUMBER	-1L

org.broadinstitute.hellbender.utils.tsv.TableUtils

Modifier and Type	Constant Field	Value
public static final char	COLUMN_SEPARATOR	9
public static final java.lang.String	COMMENT_PREFIX	"#"
public static final char	ESCAPE_CHARACTER	92
public static final char	QUOTE_CHARACTER	34
public static final java.lang.String	SAMPLE_METADATA_TAG	"SAMPLE"

org.broadinstitute.hellbender.utils.tsv.TableWriter<R>

Modifier and Type	Constant Field	Value
public static final java.lang.String	METADATA_TAG	"<METADATA>"

org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_PLOIDY	2
public static final java.lang.String	MERGE_FILTER_IN_ALL	"FilteredInAll"
public static final java.lang.String	MERGE_FILTER_PREFIX	"filterIn"
public static final java.lang.String	MERGE_INTERSECTION	"Intersection"
public static final java.lang.String	MERGE_REF_IN_ALL	"ReferenceInAlln"
public static final double	SUM_GL_THRESH_NOCALL	-0.1

org.broadinstitute.hellbender.utils.variant.GATKVCFConstants

Modifier and Type	Constant Field	Value
public static final java.lang.String	AC_ADJUSTED_KEY	"AC_adj"
public static final java.lang.String	ALIGNMENT_ARTIFACT_FILTER_NAME	"alignment"
public static final java.lang.String	ALIGNMENT_SCORE_DIFFERENCE_KEY	"ALIGN_DIFF"
public static final java.lang.String	ALLELE_BALANCE_KEY	"AB"
public static final java.lang.String	ALLELE_FRACTION_FILTER_NAME	"low_allele_frac"
public static final java.lang.String	ALLELE_FRACTION_KEY	"AF"
public static final java.lang.String	ALLELE_SPECIFIC_ANNOTATION_PREFIX	"AS"
public static final java.lang.String	ALLELE_SPECIFIC_PREFIX	"AS_"
public static final java.lang.String	ARTIFACT_IN_NORMAL_FILTER_NAME	"normal_artifact"
public static final java.lang.String	AS_ALT_ALLELE_DEPTH_KEY	"AS_AltDP"
public static final java.lang.String	AS_BASE_QUAL_RANK_SUM_KEY	"AS_BaseQRankSum"
public static final java.lang.String	AS_CULPRIT_KEY	"AS_culprit"
public static final java.lang.String	AS_FILTER_STATUS_KEY	"AS_FilterStatus"
public static final java.lang.String	AS_FISHER_STRAND_KEY	"AS_FS"
public static final java.lang.String	AS_INBREEDING_COEFFICIENT_KEY	"AS_InbreedingCoeff"
public static final java.lang.String	AS_MAP_QUAL_RANK_SUM_KEY	"AS_MQRankSum"
public static final java.lang.String	AS_QUAL_BY_DEPTH_KEY	"AS_QD"
public static final java.lang.String	AS_QUAL_KEY	"AS_QUAL"
public static final java.lang.String	AS_RAW_BASE_QUAL_RANK_SUM_KEY	"AS_RAW_BaseQRankSum"
public static final java.lang.String	AS_RAW_MAP_QUAL_RANK_SUM_KEY	"AS_RAW_MQRankSum"
public static final java.lang.String	AS_RAW_QUAL_APPROX_KEY	"AS_QUALapprox"
public static final java.lang.String	AS_RAW_READ_POS_RANK_SUM_KEY	"AS_RAW_ReadPosRankSum"
public static final java.lang.String	AS_RAW_RMS_MAPPING_QUALITY_KEY	"AS_RAW_MQ"
public static final java.lang.String	AS_READ_POS_RANK_SUM_KEY	"AS_ReadPosRankSum"
public static final java.lang.String	AS_RMS_MAPPING_QUALITY_KEY	"AS_MQ"
public static final java.lang.String	AS_SB_TABLE_KEY	"AS_SB_TABLE"
public static final java.lang.String	AS_STRAND_ODDS_RATIO_KEY	"AS_SOR"
public static final java.lang.String	AS_UNIQUE_ALT_READ_SET_COUNT_KEY	"AS_UNIQ_ALT_READ_COUNT"
public static final java.lang.String	AS_VARIANT_DEPTH_KEY	"AS_VarDP"
public static final java.lang.String	AS_VQS_LOD_KEY	"AS_VQSLOD"
public static final java.lang.String	ASSEMBLY_NAME_KEY	"assembly"
public static final java.lang.String	BAD_HAPLOTYPE_FILTER_NAME	"haplotype"
public static final java.lang.String	BASE_QUAL_HISTOGRAM_KEY	"BQHIST"
public static final java.lang.String	BASE_QUAL_RANK_SUM_KEY	"BaseQRankSum"
public static final java.lang.String	CLIPPING_RANK_SUM_KEY	"ClippingRankSum"
public static final java.lang.String	CLUSTERED_EVENTS_FILTER_NAME	"clustered_events"
public static final java.lang.String	CNN_1D_KEY	"CNN_1D"
public static final java.lang.String	CNN_2D_KEY	"CNN_2D"
public static final java.lang.String	CONTAMINATION_FILTER_NAME	"contamination"
public static final java.lang.String	CONTAMINATION_QUAL_KEY	"CONTQ"
public static final java.lang.String	CONTIG_ID_KEY	"ID"
public static final java.lang.String	CONTIG_LENGTH_KEY	"length"
public static final java.lang.String	CONVERTED_BASE_COVERAGE_KEY	"CONVERTED_BASE_COV"
public static final java.lang.String	CULPRIT_KEY	"culprit"
public static final java.lang.String	DOWNSAMPLED_KEY	"DS"
public static final java.lang.String	DUPLICATED_EVIDENCE_FILTER_NAME	"duplicate"
public static final java.lang.String	EVENT_COUNT_IN_HAPLOTYPE_KEY	"ECNT"
public static final java.lang.String	EXCESS_HET_KEY	"ExcessHet"
public static final java.lang.String	F1R2_KEY	"F1R2"
public static final java.lang.String	F2R1_KEY	"F2R1"
public static final java.lang.String	FAIL	"FAIL"
public static final java.lang.String	FEATURIZED_READ_SETS_KEY	"FRS"
public static final java.lang.String	FISHER_STRAND_KEY	"FS"
public static final java.lang.String	FRAGMENT_ALLELE_DEPTHS	"FAD"
public static final java.lang.String	GENOTYPE_AND_VALIDATE_STATUS_KEY	"callStatus"
public static final java.lang.String	GENOTYPE_PRIOR_KEY	"PG"
public static final java.lang.String	GENOTYPE_QUALITY_BY_ALLELE_BALANCE	"ABGQ"
public static final java.lang.String	GENOTYPE_QUALITY_BY_ALT_CONFIDENCE	"ALTGQ"
public static final java.lang.String	GERMLINE_QUAL_KEY	"GERMQ"
public static final java.lang.String	GERMLINE_RISK_FILTER_NAME	"germline"
public static final java.lang.String	GQ_MEAN_KEY	"GQ_MEAN"
public static final java.lang.String	GQ_STDEV_KEY	"GQ_STDDEV"
public static final java.lang.String	HAPLOTYPE_CALLER_PHASING_GT_KEY	"PGT"
public static final java.lang.String	HAPLOTYPE_CALLER_PHASING_ID_KEY	"PID"
public static final java.lang.String	HAPLOTYPE_COMPLEXITY_KEY	"HAPCOMP"
public static final java.lang.String	HAPLOTYPE_DOMINANCE_KEY	"HAPDOM"
public static final java.lang.String	HAPLOTYPE_EQUIVALENCE_COUNTS_KEY	"HEC"
public static final java.lang.String	HAPLOTYPE_SCORE_KEY	"HaplotypeScore"
public static final java.lang.String	HI_CONF_DENOVO_KEY	"hiConfDeNovo"
public static final java.lang.String	IN_PON_KEY	"PON"
public static final java.lang.String	INBREEDING_COEFFICIENT_KEY	"InbreedingCoeff"
public static final java.lang.String	INTERVAL_GC_CONTENT_KEY	"IGC"
public static final java.lang.String	JOINT_ALIGNMENT_COUNT_KEY	"NALIGNS"
public static final java.lang.String	JOINT_LIKELIHOOD_TAG_NAME	"JL"
public static final java.lang.String	JOINT_POSTERIOR_TAG_NAME	"JP"
public static final java.lang.String	LIKELIHOOD_RANK_SUM_KEY	"LikelihoodRankSum"
public static final java.lang.String	LO_CONF_DENOVO_KEY	"loConfDeNovo"
public static final java.lang.String	LOW_HET_FILTER_NAME	"mt_many_low_hets"
public static final java.lang.String	LOW_QUAL_FILTER_NAME	"LowQual"
public static final java.lang.String	MAP_QUAL_RANK_SUM_KEY	"MQRankSum"
public static final java.lang.String	MAPPING_QUALITY_DEPTH_DEPRECATED	"MQ_DP"
public static final java.lang.String	MAPPING_QUALITY_ZERO_BY_SAMPLE_KEY	"MQ0"
public static final java.lang.String	MEDIAN_BASE_QUALITY_FILTER_NAME	"base_qual"
public static final java.lang.String	MEDIAN_BASE_QUALITY_KEY	"MBQ"
public static final java.lang.String	MEDIAN_FRAGMENT_LENGTH_DIFFERENCE_FILTER_NAME	"fragment"
public static final java.lang.String	MEDIAN_FRAGMENT_LENGTH_KEY	"MFRL"
public static final java.lang.String	MEDIAN_MAPPING_QUALITY_FILTER_NAME	"map_qual"
public static final java.lang.String	MEDIAN_MAPPING_QUALITY_KEY	"MMQ"
public static final java.lang.String	MEDIAN_READ_POSITON_KEY	"MPOS"
public static final java.lang.String	METHYLATION_REFERENCE_CONTEXT_KEY	"REFERENCE_CONTEXT"
public static final java.lang.String	MIN_DP_FORMAT_KEY	"MIN_DP"
public static final java.lang.String	MLE_ALLELE_COUNT_KEY	"MLEAC"
public static final java.lang.String	MLE_ALLELE_FREQUENCY_KEY	"MLEAF"
public static final java.lang.String	MULTIALLELIC_FILTER_NAME	"multiallelic"
public static final java.lang.String	N_COUNT_KEY	"NCount"
public static final java.lang.String	N_RATIO_FILTER_NAME	"n_ratio"
public static final java.lang.String	NEGATIVE_LABEL_KEY	"NEGATIVE_TRAIN_SITE"
public static final java.lang.String	NOCALL_CHROM_KEY	"NCC"
public static final java.lang.String	NON_REF_SYMBOLIC_ALLELE_NAME	"NON_REF"
public static final java.lang.String	NORMAL_ARTIFACT_LOG_10_ODDS_KEY	"NALOD"
public static final java.lang.String	NORMAL_LOG_10_ODDS_KEY	"NLOD"
public static final java.lang.String	NUMBER_OF_DISCOVERED_ALLELES_KEY	"NDA"
public static final java.lang.String	ORIGINAL_AC_KEY	"AC_Orig"
public static final java.lang.String	ORIGINAL_AF_KEY	"AF_Orig"
public static final java.lang.String	ORIGINAL_AN_KEY	"AN_Orig"
public static final java.lang.String	ORIGINAL_CONTIG_MISMATCH_KEY	"OCM"
public static final java.lang.String	ORIGINAL_DP_KEY	"DP_Orig"
public static final java.lang.String	PHRED_SCALED_POSTERIORS_KEY	"PP"
public static final java.lang.String	POLYMERASE_SLIPPAGE	"slippage"
public static final java.lang.String	POLYMERASE_SLIPPAGE_QUAL_KEY	"STRQ"
public static final java.lang.String	PON_FILTER_NAME	"panel_of_normals"
public static final java.lang.String	POPULATION_AF_KEY	"POPAF"
public static final java.lang.String	POSITIVE_LABEL_KEY	"POSITIVE_TRAIN_SITE"
public static final java.lang.String	POSSIBLE_NUMT_FILTER_NAME	"possible_numt"
public static final java.lang.String	PSEUDO_DEPTH_KEY	"DD"
public static final java.lang.String	PSEUDO_FRACTION_KEY	"DF"
public static final java.lang.String	QUAL_BY_DEPTH_KEY	"QD"
public static final java.lang.String	RAW_GENOTYPE_COUNT_KEY	"RAW_GT_COUNT"
public static final java.lang.String	RAW_MAP_QUAL_RANK_SUM_KEY	"RAW_MQRankSum"
public static final java.lang.String	RAW_MAPPING_QUALITY_WITH_DEPTH_KEY	"RAW_MQandDP"
public static final java.lang.String	RAW_QUAL_APPROX_KEY	"QUALapprox"
public static final java.lang.String	RAW_RMS_MAPPING_QUALITY_DEPRECATED	"RAW_MQ"
public static final java.lang.String	READ_ORIENTATION_ARTIFACT_FILTER_NAME	"orientation"
public static final java.lang.String	READ_ORIENTATION_QUAL_KEY	"ROQ"
public static final java.lang.String	READ_POS_RANK_SUM_KEY	"ReadPosRankSum"
public static final java.lang.String	READ_POSITION_FILTER_NAME	"position"
public static final java.lang.String	REFERENCE_BASES_KEY	"REF_BASES"
public static final java.lang.String	REFERENCE_GENOTYPE_QUALITY	"RGQ"
public static final java.lang.String	REPEAT_UNIT_KEY	"RU"
public static final java.lang.String	REPEATS_PER_ALLELE_KEY	"RPA"
public static final java.lang.String	SAMPLE_LIST_KEY	"Samples"
public static final java.lang.String	SB_TABLE_KEY	"SB_TABLE"
public static final java.lang.String	SEQUENCING_QUAL_KEY	"SEQQ"
public static final java.lang.String	SITE_LEVEL_FILTERS	"SITE"
public static final java.lang.String	SPANNING_DELETION_SYMBOLIC_ALLELE_NAME_DEPRECATED	"*:DEL"
public static final java.lang.String	STR_PRESENT_KEY	"STR"
public static final java.lang.String	STRAND_ARTIFACT_FILTER_NAME	"strand_bias"
public static final java.lang.String	STRAND_BIAS_BY_SAMPLE_KEY	"SB"
public static final java.lang.String	STRAND_COUNT_BY_SAMPLE_KEY	"SAC"
public static final java.lang.String	STRAND_ODDS_RATIO_KEY	"SOR"
public static final java.lang.String	STRAND_QUAL_KEY	"STRANDQ"
public static final java.lang.String	STRICT_STRAND_BIAS_FILTER_NAME	"strict_strand"
public static final java.lang.String	SYMBOLIC_ALLELE_DEFINITION_HEADER_TAG	"ALT"
public static final java.lang.String	TRANSMISSION_PROBABILITY_KEY	"TP"
public static final java.lang.String	TUMOR_EVIDENCE_FILTER_NAME	"weak_evidence"
public static final java.lang.String	TUMOR_LOG_10_ODDS_KEY	"TLOD"
public static final java.lang.String	UNCONVERTED_BASE_COVERAGE_KEY	"UNCONVERTED_BASE_COV"
public static final java.lang.String	UNITIG_SIZES_KEY	"UNITIGS"
public static final java.lang.String	VARIANT_DEPTH_KEY	"VarDP"
public static final java.lang.String	VQS_LOD_KEY	"VQSLOD"

org.broadinstitute.hellbender.utils.variant.HomoSapiensConstants

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_PLOIDY	2
public static final double	INDEL_HETEROZYGOSITY	1.25E-4
public static final double	SNP_HETEROZYGOSITY	0.001

org.broadinstitute.hellbender.utils.variant.VcfUtils

Modifier and Type	Constant Field	Value
public static final java.lang.String	BCF_FILE_EXTENSION	"bcf"
public static final java.lang.String	VCF_FILE_EXTENSION	"vcf"

org.broadinstitute.hellbender.utils.variant.writers.GVCFWriter

Modifier and Type	Constant Field	Value
public static final java.lang.String	GVCF_BLOCK	"GVCFBlock"

org.broadinstitute.hellbender.utils.variant.writers.ShardingVCFWriter

Modifier and Type	Constant Field	Value
public static final java.lang.String	SHARD_INDEX_PREFIX	".shard_"
public static final java.lang.String	SHARD_INDEX_SUFFIX	".vcf.gz"

picard.analysis.*

picard.analysis.CollectInsertSizeMetrics

Modifier and Type	Constant Field	Value
protected static final java.lang.String	Histogram_R_SCRIPT	"picard/analysis/insertSizeHistogram.R"

picard.analysis.CollectRrbsMetrics

Modifier and Type	Constant Field	Value
public static final java.lang.String	DETAIL_FILE_EXTENSION	"rrbs_detail_metrics"
public static final java.lang.String	PDF_FILE_EXTENSION	"rrbs_qc.pdf"
public static final java.lang.String	SUMMARY_FILE_EXTENSION	"rrbs_summary_metrics"

picard.analysis.artifacts.CollectSequencingArtifactMetrics

Modifier and Type	Constant Field	Value
public static final java.lang.String	USAGE_SUMMARY	"Collect metrics to quantify single-base sequencing artifacts. "

picard.analysis.artifacts.ConvertSequencingArtifactToOxoG

Modifier and Type	Constant Field	Value
public static final java.lang.String	OXOG_METRICS_EXT	".oxog_metrics"

picard.analysis.artifacts.SequencingArtifactMetrics

Modifier and Type	Constant Field	Value
public static final java.lang.String	BAIT_BIAS_DETAILS_EXT	".bait_bias_detail_metrics"
public static final java.lang.String	BAIT_BIAS_SUMMARY_EXT	".bait_bias_summary_metrics"
public static final java.lang.String	ERROR_SUMMARY_EXT	".error_summary_metrics"
public static final java.lang.String	PRE_ADAPTER_DETAILS_EXT	".pre_adapter_detail_metrics"
public static final java.lang.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 java.lang.String	FILE_EXTENSION	"bafregress_metrics"

picard.arrays.CreateVerifyIDIntensityContaminationMetricsFile

Modifier and Type	Constant Field	Value
public static final java.lang.String	FILE_EXTENSION	"verifyidintensity_metrics"

picard.arrays.illumina.IlluminaManifest

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

picard.arrays.illumina.IlluminaManifestRecord

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

picard.cmdline.*

picard.cmdline.StandardOptionDefinitions

Modifier and Type	Constant Field	Value
public static final java.lang.String	ASSUME_SORT_ORDER_SHORT_NAME	"ASO"
public static final java.lang.String	ASSUME_SORTED_SHORT_NAME	"AS"
public static final java.lang.String	EXPECTED_INSERT_SIZE_SHORT_NAME	"INSERT"
public static final java.lang.String	INPUT_SHORT_NAME	"I"
public static final java.lang.String	LANE_SHORT_NAME	"L"
public static final java.lang.String	LIBRARY_NAME_SHORT_NAME	"LIB"
public static final java.lang.String	METRICS_FILE_SHORT_NAME	"M"
public static final java.lang.String	MINIMUM_LOD_SHORT_NAME	"LOD"
public static final java.lang.String	MINIMUM_MAPPING_QUALITY_SHORT_NAME	"MQ"
public static final java.lang.String	OUTPUT_SHORT_NAME	"O"
public static final java.lang.String	PF_READS_ONLY_SHORT_NAME	"PF"
public static final java.lang.String	PROGRAM_RECORD_ID_SHORT_NAME	"PG"
public static final java.lang.String	READ_GROUP_ID_SHORT_NAME	"RG"
public static final java.lang.String	REFERENCE_SHORT_NAME	"R"
public static final java.lang.String	SAMPLE_ALIAS_SHORT_NAME	"ALIAS"
public static final java.lang.String	SEQUENCE_DICTIONARY_SHORT_NAME	"SD"
public static final java.lang.String	SORT_ORDER_SHORT_NAME	"SO"
public static final java.lang.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 java.lang.String	FINGERPRINT_DETAIL_FILE_SUFFIX	"fingerprinting_detail_metrics"
public static final java.lang.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 java.lang.String	HET_GENOTYPE_FOR_PHASING	"HetGenotypeForPhasing"
public static final java.lang.String	PHASESET_PREFIX	"PhaseSet"
public static final java.lang.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.ExtractIlluminaBarcodes

Modifier and Type	Constant Field	Value
public static final java.lang.String	BARCODE_NAME_COLUMN	"barcode_name"
public static final java.lang.String	BARCODE_SEQUENCE_1_COLUMN	"barcode_sequence_1"
public static final java.lang.String	BARCODE_SEQUENCE_COLUMN	"barcode_sequence"
public static final java.lang.String	LIBRARY_NAME_COLUMN	"library_name"

picard.illumina.IlluminaBasecallsToSam

Modifier and Type	Constant Field	Value
public static final java.lang.String	USAGE	"Generate a SAM or BAM 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 java.lang.String	PER_TILE_PATTERN_STRING	"s_(\\d+)_(\\d{1,5})"

picard.illumina.parser.ReadStructure

Modifier and Type	Constant Field	Value
public static final java.lang.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 java.lang.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 java.lang.String	detailedMetricsExtension	".pffail_detailed_metrics"
public static final java.lang.String	summaryMetricsExtension	".pffail_summary_metrics"

picard.metrics.*

picard.metrics.MultiLevelCollector<METRIC_TYPE extends htsjdk.samtools.metrics.MetricBase,Histogram_KEY extends java.lang.Comparable,ARGTYPE>

Modifier and Type	Constant Field	Value
public static final java.lang.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 java.lang.String	READGROUP_ID_REGEX	"^[ -~]+$"

picard.sam.DownsampleSam

Modifier and Type	Constant Field	Value
public static final java.lang.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 java.lang.String	DUPLICATE_SET_INDEX_TAG	"DI"
public static final java.lang.String	DUPLICATE_SET_SIZE_TAG	"DS"
public static final java.lang.String	DUPLICATE_TYPE_LIBRARY	"LB"
public static final java.lang.String	DUPLICATE_TYPE_SEQUENCING	"SQ"
public static final java.lang.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 java.lang.String	BARCODE_DELIMITER	"-"

picard.util.LiftoverUtils

Modifier and Type	Constant Field	Value
public static final java.lang.String	REV_COMPED_ALLELES	"ReverseComplementedAlleles"
public static final java.lang.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 java.lang.String	DOC_CAT_BASE_CALLING	"Base Calling"
public static final java.lang.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 java.lang.String	DOC_CAT_DIAGNOSTICS_AND_QC	"Diagnostics and Quality Control"
public static final java.lang.String	DOC_CAT_DIAGNOSTICS_AND_QC_SUMMARY	"Tools that collect sequencing quality related and comparative metrics"
public static final java.lang.String	DOC_CAT_GENOTYPING_ARRAYS_MANIPULATION	"Genotyping Arrays Manipulation"
public static final java.lang.String	DOC_CAT_GENOTYPING_ARRAYS_MANIPULATION_SUMMARY	"Tools that manipulate data generated by Genotyping arrays"
public static final java.lang.String	DOC_CAT_INTERVALS_MANIPULATION	"Intervals Manipulation"
public static final java.lang.String	DOC_CAT_INTERVALS_MANIPULATION_SUMMARY	"Tools that process genomic intervals in various formats"
public static final java.lang.String	DOC_CAT_OTHER	"Other"
public static final java.lang.String	DOC_CAT_OTHER_SUMMARY	"Miscellaneous tools, e.g. those that aid in data streaming"
public static final java.lang.String	DOC_CAT_READ_DATA_MANIPULATION	"Read Data Manipulation"
public static final java.lang.String	DOC_CAT_READ_DATA_MANIPULATION_SUMMARY	"Tools that manipulate read data in SAM, BAM or CRAM format"
public static final java.lang.String	DOC_CAT_REFERENCE	"Reference"
public static final java.lang.String	DOC_CAT_REFERENCE_SUMMARY	"Tools that analyze and manipulate FASTA format references"
public static final java.lang.String	DOC_CAT_TEST	"Test Tools"
public static final java.lang.String	DOC_CAT_TEST_SUMMARY	"Tools for internal test purposes"
public static final java.lang.String	DOC_CAT_VARIANT_EVALUATION	"Variant Evaluation and Refinement"
public static final java.lang.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 java.lang.String	DOC_CAT_VARIANT_FILTERING	"Variant Filtering"
public static final java.lang.String	DOC_CAT_VARIANT_FILTERING_SUMMARY	"Tools that filter variants by annotating the FILTER column"
public static final java.lang.String	DOC_CAT_VARIANT_MANIPULATION	"Variant Manipulation"
public static final java.lang.String	DOC_CAT_VARIANT_MANIPULATION_SUMMARY	"Tools that manipulate variant call format (VCF) data"
public static final java.lang.String	DOC_SUPERCAT_EXCLUDE	"exclude"
public static final java.lang.String	DOC_SUPERCAT_TOOLS	"tools"
public static final java.lang.String	DOC_SUPERCAT_UTILITIES	"utilities"

picard.vcf.*

picard.vcf.GenotypeConcordance

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

picard.vcf.LiftoverVcf

Modifier and Type	Constant Field	Value
public static final java.lang.String	ATTEMPTED_ALLELES	"AttemptedAlleles"
public static final java.lang.String	ATTEMPTED_LOCUS	"AttemptedLocus"
public static final java.lang.String	FILTER_CANNOT_LIFTOVER_REV_COMP	"CannotLiftOver"
public static final java.lang.String	FILTER_INDEL_STRADDLES_TWO_INTERVALS	"IndelStraddlesMultipleIntevals"
public static final java.lang.String	FILTER_MISMATCHING_REF_ALLELE	"MismatchedRefAllele"
public static final java.lang.String	FILTER_NO_TARGET	"NoTarget"
public static final java.lang.String	ORIGINAL_ALLELES	"OriginalAlleles"
public static final java.lang.String	ORIGINAL_CONTIG	"OriginalContig"
public static final java.lang.String	ORIGINAL_START	"OriginalStart"

picard.vcf.VcfToIntervalList

Modifier and Type	Constant Field	Value
public static final java.lang.String	INCLUDE_FILTERED_SHORT_NAME	"IF"

picard.vcf.filter.AlleleBalanceFilter

Modifier and Type	Constant Field	Value
public static final java.lang.String	AB_FILTER	"AlleleBalance"

picard.vcf.filter.FilterApplyingVariantIterator

Modifier and Type	Constant Field	Value
public static final java.lang.String	ALL_GTS_FILTERED	"AllGtsFiltered"
public static final java.lang.String	PASS_FILTER	"PASS"

picard.vcf.filter.QdFilter

Modifier and Type	Constant Field	Value
public static final java.lang.String	FILTER_NAME	"LowQD"