Constant Field Values
Contents
picard.analysis.*
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picard.analysis.CollectInsertSizeMetrics Modifier and Type Constant Field Value protected static final String
Histogram_R_SCRIPT
"picard/analysis/insertSizeHistogram.R"
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picard.analysis.CollectRrbsMetrics Modifier and Type Constant Field Value public static final String
DETAIL_FILE_EXTENSION
"rrbs_detail_metrics"
public static final String
PDF_FILE_EXTENSION
"rrbs_qc.pdf"
public static final String
SUMMARY_FILE_EXTENSION
"rrbs_summary_metrics"
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picard.analysis.artifacts.CollectSequencingArtifactMetrics Modifier and Type Constant Field Value public static final String
USAGE_SUMMARY
"Collect metrics to quantify single-base sequencing artifacts. "
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picard.analysis.artifacts.ConvertSequencingArtifactToOxoG Modifier and Type Constant Field Value public static final String
OXOG_METRICS_EXT
".oxog_metrics"
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picard.analysis.artifacts.SequencingArtifactMetrics Modifier and Type Constant Field Value public static final String
BAIT_BIAS_DETAILS_EXT
".bait_bias_detail_metrics"
public static final String
BAIT_BIAS_SUMMARY_EXT
".bait_bias_summary_metrics"
public static final String
ERROR_SUMMARY_EXT
".error_summary_metrics"
public static final String
PRE_ADAPTER_DETAILS_EXT
".pre_adapter_detail_metrics"
public static final String
PRE_ADAPTER_SUMMARY_EXT
".pre_adapter_summary_metrics"
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picard.analysis.directed.RnaSeqMetricsCollector Modifier and Type Constant Field Value public static final int
defaultEndBiasBases
100
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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.*
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picard.arrays.CreateBafRegressMetricsFile Modifier and Type Constant Field Value public static final String
FILE_EXTENSION
"bafregress_metrics"
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picard.arrays.CreateVerifyIDIntensityContaminationMetricsFile Modifier and Type Constant Field Value public static final String
FILE_EXTENSION
"verifyidintensity_metrics"
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picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator Modifier and Type Constant Field Value public static final String
ACGT_CODES
"ACGTacgt"
public static final String
BUILD_37
"37"
public static final int
FIVE_PRIME_SEQUENCE
1
public static final int
INDEL_SEQUENCE
3
public static final String
IUPAC_NUCLEOTIDE_CODES
"ACGTRYSWKMBDHVNacgtryswkmbdhvn"
public static final int
PRE_INDEL_SEQUENCE
2
public static final int
THREE_PRIME_SEQUENCE
4
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picard.arrays.illumina.IlluminaManifest Modifier and Type Constant Field Value public static final String
ADDRESS_A_ID_HEADER_NAME
"AddressA_ID"
public static final String
ADDRESS_B_ID_HEADER_NAME
"AddressB_ID"
public static final String
ALLELE_A_PROBE_SEQ_HEADER_NAME
"AlleleA_ProbeSeq"
public static final String
ALLELE_B_PROBE_SEQ_HEADER_NAME
"AlleleB_ProbeSeq"
public static final String
BEAD_SET_ID_HEADER_NAME
"BeadSetID"
public static final String
CHROMOSOME_HEADER_NAME
"Chr"
public static final String
EXP_CLUSTERS_HEADER_NAME
"Exp_Clusters"
public static final String
GENOME_BUILD_HEADER_NAME
"GenomeBuild"
public static final String
HG17
"HG17"
public static final String
HG18
"HG18"
public static final String
HG19
"HG19"
public static final String
ILLUMINA_ID_HEADER_NAME
"IlmnID"
public static final String
ILLUMINA_STRAND_HEADER_NAME
"IlmnStrand"
public static final String
INTENSITY_ONLY_HEADER_NAME
"Intensity_Only"
public static final String
MAP_INFO_HEADER_NAME
"MapInfo"
public static final String
NAME_HEADER_NAME
"Name"
public static final String
NCBI_35
"35"
public static final String
NCBI_36
"36"
public static final String
NCBI_37
"37"
public static final String
PLOIDY_HEADER_NAME
"Ploidy"
public static final String
REF_STRAND_HEADER_NAME
"RefStrand"
public static final String
SNP_HEADER_NAME
"SNP"
public static final String
SOURCE_HEADER_NAME
"Source"
public static final String
SOURCE_SEQ_HEADER_NAME
"SourceSeq"
public static final String
SOURCE_STRAND_HEADER_NAME
"SourceStrand"
public static final String
SOURCE_VERSION_HEADER_NAME
"SourceVersion"
public static final String
SPECIES_HEADER_NAME
"Species"
public static final String
TOP_GENOMIC_SEQ_HEADER_NAME
"TopGenomicSeq"
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picard.arrays.illumina.IlluminaManifestRecord Modifier and Type Constant Field Value public static final String
ILLUMINA_FLAGGED_BAD_CHR
"0"
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picard.arrays.illumina.InfiniumDataFile Modifier and Type Constant Field Value public static final int
MAX_UNSIGNED_SHORT
65535
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picard.arrays.illumina.InfiniumEGTFile Modifier and Type Constant Field Value public static final String
EXTENSION
"egt"
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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
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picard.arrays.illumina.InfiniumVcfFields Modifier and Type Constant Field Value public static final String
ALLELE_A
"ALLELE_A"
public static final String
ALLELE_B
"ALLELE_B"
public static final String
ANALYSIS_VERSION_NUMBER
"analysisVersionNumber"
public static final String
ARRAY_TYPE
"arrayType"
public static final String
AUTOCALL_DATE
"autocallDate"
public static final String
AUTOCALL_GENDER
"autocallGender"
public static final String
AUTOCALL_VERSION
"autocallVersion"
public static final String
BAF
"BAF"
public static final String
BEADSET_ID
"BEADSET_ID"
public static final String
CHIP_WELL_BARCODE
"chipWellBarcode"
public static final String
CLUSTER_FILE
"clusterFile"
public static final String
DUPE
"DUPE"
public static final String
EXPECTED_GENDER
"expectedGender"
public static final String
EXTENDED_ILLUMINA_MANIFEST_FILE
"extendedManifestFile"
public static final String
EXTENDED_ILLUMINA_MANIFEST_VERSION
"extendedIlluminaManifestVersion"
public static final String
FAIL_REF
"FAIL_REF"
public static final String
FINGERPRINT_GENDER
"fingerprintGender"
public static final String
GC_SCORE
"GC_SCORE"
public static final String
GTA
"GTA"
public static final String
GTC_CALL_RATE
"gtcCallRate"
public static final String
GTC_CALL_RATE_DETAIL
"gtcCallRateDetail"
public static final String
GTZ
"GTZ"
public static final String
IGC
"IGC"
public static final String
ILLUMINA_BUILD
"ILLUMINA_BUILD"
public static final String
ILLUMINA_CHR
"ILLUMINA_CHR"
public static final String
ILLUMINA_POS
"ILLUMINA_POS"
public static final String
ILLUMINA_STRAND
"ILLUMINA_STRAND"
public static final String
IMAGING_DATE
"imagingDate"
public static final String
LRR
"LRR"
public static final String
MANIFEST_FILE
"manifestFile"
public static final String
NORMX
"NORMX"
public static final String
NORMY
"NORMY"
public static final String
P_95_GREEN
"p95Green"
public static final String
P_95_RED
"p95Red"
public static final String
PIPELINE_VERSION
"pipelineVersion"
public static final String
PROBE_A
"PROBE_A"
public static final String
PROBE_B
"PROBE_B"
public static final String
R
"R"
public static final String
RS_ID
"refSNP"
public static final String
SAMPLE_ALIAS
"sampleAlias"
public static final String
SCANNER_NAME
"scannerName"
public static final String
SOURCE
"SOURCE"
public static final String
THETA
"THETA"
public static final String
TRIALLELIC
"TRIALLELIC"
public static final String
X
"X"
public static final String
Y
"Y"
public static final String
ZCALL_THRESHOLDS
"zcallThresholds"
public static final String
ZCALL_VERSION
"zcallVersion"
public static final String
ZEROED_OUT_ASSAY
"ZEROED_OUT_ASSAY"
public static final String
ZTHRESH_X
"zthresh_X"
public static final String
ZTHRESH_Y
"zthresh_Y"
picard.cmdline.*
picard.fingerprint.*
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picard.fingerprint.CalculateFingerprintMetrics Modifier and Type Constant Field Value public final double
GENOTYPE_LOD_THRESHOLD
3.0
public final int
NUMBER_OF_SAMPLING
100
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picard.fingerprint.CheckFingerprint Modifier and Type Constant Field Value public static final String
FINGERPRINT_DETAIL_FILE_SUFFIX
"fingerprinting_detail_metrics"
public static final String
FINGERPRINT_SUMMARY_FILE_SUFFIX
"fingerprinting_summary_metrics"
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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
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picard.fingerprint.HaplotypeMap Modifier and Type Constant Field Value public static final String
HET_GENOTYPE_FOR_PHASING
"HetGenotypeForPhasing"
public static final String
PHASESET_PREFIX
"PhaseSet"
public static final String
SYNTHETIC_PHASESET_PREFIX
"Synthetic"
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picard.fingerprint.LiftOverHaplotypeMap Modifier and Type Constant Field Value public static final int
LIFTOVER_FAILED_FOR_ONE_OR_MORE_SNPS
101
picard.illumina.*
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picard.illumina.ExtractBarcodesProgram Modifier and Type Constant Field Value public static final String
BARCODE_COLUMN
"barcode"
public static final String
BARCODE_NAME_COLUMN
"barcode_name"
public static final String
BARCODE_SEQUENCE_COLUMN
"barcode_sequence"
public static final String
LIBRARY_NAME_COLUMN
"library_name"
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picard.illumina.IlluminaBasecallsToSam Modifier and Type Constant Field Value public static final String
USAGE
"Generate a SAM, BAM or CRAM file from data in an Illumina basecalls output directory"
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picard.illumina.parser.MultiTileBclParser Modifier and Type Constant Field Value public static final byte
MASKING_QUALITY
2
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picard.illumina.parser.ParameterizedFileUtil Modifier and Type Constant Field Value protected static final boolean
DefaultSkipEmptyFiles
true
public static final String
PER_TILE_PATTERN_STRING
"s_(\\d+)_(\\d{1,5})"
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picard.illumina.parser.ReadStructure Modifier and Type Constant Field Value public static final String
PARAMETER_DOC
"A description of the logical structure of clusters in an Illumina Run, i.e. a description of the structure IlluminaBasecallsToSam assumes the data to be in. It should consist of integer/character pairs describing the number of cycles and the type of those cycles (B for Sample Barcode, M for molecular barcode, T for Template, and S for skip). E.g. If the input data consists of 80 base clusters and we provide a read structure of \"28T8M8B8S28T\" then the sequence may be split up into four reads:\n* read one with 28 cycles (bases) of template\n* read two with 8 cycles (bases) of molecular barcode (ex. unique molecular barcode)\n* read three with 8 cycles (bases) of sample barcode\n* 8 cycles (bases) skipped.\n* read four with 28 cycles (bases) of template\nThe skipped cycles would NOT be included in an output SAM/BAM file or in read groups therein."
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picard.illumina.parser.readers.AbstractIlluminaPositionFileReader Modifier and Type Constant Field Value public static final float
MAX_POS
1.0E7f
public static final float
MIN_POS
-10.0f
public static final String
S_LOCS_FILE
"s.locs"
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picard.illumina.parser.readers.BaseBclReader Modifier and Type Constant Field Value public static final byte
NO_CALL_BASE
78
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picard.illumina.parser.readers.BclQualityEvaluationStrategy Modifier and Type Constant Field Value public static final int
ILLUMINA_ALLEGED_MINIMUM_QUALITY
2
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picard.illumina.parser.readers.FilterFileReader Modifier and Type Constant Field Value public static final int
EXPECTED_VERSION
3
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picard.illumina.quality.CollectHiSeqXPfFailMetrics Modifier and Type Constant Field Value public static final String
detailedMetricsExtension
".pffail_detailed_metrics"
public static final String
summaryMetricsExtension
".pffail_summary_metrics"
picard.metrics.*
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picard.metrics.MultiLevelCollector<METRIC_TYPE extends htsjdk.samtools.metrics.MetricBase,Histogram_KEY extends Comparable,ARGTYPE> Modifier and Type Constant Field Value public static final String
UNKNOWN
"unknown"
picard.sam.*
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picard.sam.AbstractAlignmentMerger Modifier and Type Constant Field Value public static final int
MAX_RECORDS_IN_RAM
500000
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picard.sam.AddOrReplaceReadGroups Modifier and Type Constant Field Value public static final String
READGROUP_ID_REGEX
"^[ -~]+$"
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picard.sam.DownsampleSam Modifier and Type Constant Field Value public static final String
RANDOM_SEED_TAG
"rs"
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picard.sam.SplitSamByLibrary Modifier and Type Constant Field Value public static final int
NO_LIBRARIES_SPECIFIED_IN_HEADER
2
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picard.sam.markduplicates.MarkDuplicates Modifier and Type Constant Field Value public static final String
DUPLICATE_SET_INDEX_TAG
"DI"
public static final String
DUPLICATE_SET_SIZE_TAG
"DS"
public static final String
DUPLICATE_TYPE_LIBRARY
"LB"
public static final String
DUPLICATE_TYPE_SEQUENCING
"SQ"
public static final String
DUPLICATE_TYPE_TAG
"DT"
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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
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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
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picard.sam.markduplicates.util.ReadEndsForMarkDuplicates Modifier and Type Constant Field Value protected static final int
SIZE_OF
69
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picard.sam.SamErrorMetric.ReadBaseStratification Modifier and Type Constant Field Value public static final int
NOT_ALIGNED_ERROR
-1
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picard.sam.util.PhysicalLocation Modifier and Type Constant Field Value public static final int
NO_VALUE
-1
picard.util.*
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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
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picard.util.AsyncIterator<T> Modifier and Type Constant Field Value public static final int
DEFAULT_QUEUE_SIZE
2000
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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
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picard.util.IlluminaUtil Modifier and Type Constant Field Value public static final String
BARCODE_DELIMITER
"-"
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picard.util.LiftoverUtils Modifier and Type Constant Field Value public static final String
REV_COMPED_ALLELES
"ReverseComplementedAlleles"
public static final String
SWAPPED_ALLELES
"SwappedAlleles"
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picard.util.MathUtil Modifier and Type Constant Field Value public static final double
MAX_PROB_BELOW_ONE
0.9999999999999999
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picard.util.help.HelpConstants Modifier and Type Constant Field Value public static final String
DOC_CAT_BASE_CALLING
"Base Calling"
public static final String
DOC_CAT_BASE_CALLING_SUMMARY
"Tools that process sequencing machine data, e.g. Illumina base calls, and detect sequencing level attributes, e.g. adapters"
public static final String
DOC_CAT_DIAGNOSTICS_AND_QC
"Diagnostics and Quality Control"
public static final String
DOC_CAT_DIAGNOSTICS_AND_QC_SUMMARY
"Tools that collect sequencing quality related and comparative metrics"
public static final String
DOC_CAT_GENOTYPING_ARRAYS_MANIPULATION
"Genotyping Arrays Manipulation"
public static final String
DOC_CAT_GENOTYPING_ARRAYS_MANIPULATION_SUMMARY
"Tools that manipulate data generated by Genotyping arrays"
public static final String
DOC_CAT_INTERVALS_MANIPULATION
"Intervals Manipulation"
public static final String
DOC_CAT_INTERVALS_MANIPULATION_SUMMARY
"Tools that process genomic intervals in various formats"
public static final String
DOC_CAT_METRICS
"Metrics"
public static final String
DOC_CAT_METRICS_SUMMARY
"Metrics"
public static final String
DOC_CAT_OTHER
"Other"
public static final String
DOC_CAT_OTHER_SUMMARY
"Miscellaneous tools, e.g. those that aid in data streaming"
public static final String
DOC_CAT_READ_DATA_MANIPULATION
"Read Data Manipulation"
public static final String
DOC_CAT_READ_DATA_MANIPULATION_SUMMARY
"Tools that manipulate read data in SAM, BAM or CRAM format"
public static final String
DOC_CAT_REFERENCE
"Reference"
public static final String
DOC_CAT_REFERENCE_SUMMARY
"Tools that analyze and manipulate FASTA format references"
public static final String
DOC_CAT_TEST
"Test Tools"
public static final String
DOC_CAT_TEST_SUMMARY
"Tools for internal test purposes"
public static final String
DOC_CAT_VARIANT_EVALUATION
"Variant Evaluation and Refinement"
public static final String
DOC_CAT_VARIANT_EVALUATION_SUMMARY
"Tools that evaluate and refine variant calls, e.g. with annotations not offered by the engine"
public static final String
DOC_CAT_VARIANT_FILTERING
"Variant Filtering"
public static final String
DOC_CAT_VARIANT_FILTERING_SUMMARY
"Tools that filter variants by annotating the FILTER column"
public static final String
DOC_CAT_VARIANT_MANIPULATION
"Variant Manipulation"
public static final String
DOC_CAT_VARIANT_MANIPULATION_SUMMARY
"Tools that manipulate variant call format (VCF) data"
public static final String
DOC_SUPERCAT_EXCLUDE
"exclude"
public static final String
DOC_SUPERCAT_TOOLS
"tools"
public static final String
DOC_SUPERCAT_UTILITIES
"utilities"
picard.vcf.*
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picard.vcf.GenotypeConcordance Modifier and Type Constant Field Value public static final String
CONTINGENCY_METRICS_FILE_EXTENSION
".genotype_concordance_contingency_metrics"
public static final String
CONTINGENCY_STATE_TAG
"CONC_ST"
public static final String
DETAILED_METRICS_FILE_EXTENSION
".genotype_concordance_detail_metrics"
public static final String
OUTPUT_VCF_CALL_SAMPLE_NAME
"call"
public static final String
OUTPUT_VCF_FILE_EXTENSION
".genotype_concordance.vcf.gz"
public static final String
OUTPUT_VCF_TRUTH_SAMPLE_NAME
"truth"
public static final String
SUMMARY_METRICS_FILE_EXTENSION
".genotype_concordance_summary_metrics"
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picard.vcf.LiftoverVcf Modifier and Type Constant Field Value public static final String
ATTEMPTED_ALLELES
"AttemptedAlleles"
public static final String
ATTEMPTED_LOCUS
"AttemptedLocus"
public static final String
FILTER_CANNOT_LIFTOVER_REV_COMP
"CannotLiftOver"
public static final String
FILTER_INDEL_STRADDLES_TWO_INTERVALS
"IndelStraddlesMultipleIntevals"
public static final String
FILTER_MISMATCHING_REF_ALLELE
"MismatchedRefAllele"
public static final String
FILTER_NO_TARGET
"NoTarget"
public static final String
ORIGINAL_ALLELES
"OriginalAlleles"
public static final String
ORIGINAL_CONTIG
"OriginalContig"
public static final String
ORIGINAL_START
"OriginalStart"
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picard.vcf.VcfToIntervalList Modifier and Type Constant Field Value public static final String
INCLUDE_FILTERED_SHORT_NAME
"IF"
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picard.vcf.filter.AlleleBalanceFilter Modifier and Type Constant Field Value public static final String
AB_FILTER
"AlleleBalance"
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picard.vcf.filter.FilterApplyingVariantIterator Modifier and Type Constant Field Value public static final String
ALL_GTS_FILTERED
"AllGtsFiltered"
public static final String
PASS_FILTER
"PASS"
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picard.vcf.filter.QdFilter Modifier and Type Constant Field Value public static final String
FILTER_NAME
"LowQD"