org.broadinstitute.hellbender.utils.variant

Class GATKVCFConstants

java.lang.Object

org.broadinstitute.hellbender.utils.variant.GATKVCFConstants

public final class GATKVCFConstants
extends java.lang.Object

This class contains any constants (primarily FORMAT/INFO keys) in VCF files used by the GATK. Note that VCF-standard constants are in VCFConstants, in htsjdk. Keys in header lines should have matching entries in GATKVCFHeaderLines

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	AC_ADJUSTED_KEY
static java.lang.String	ALIGNMENT_ARTIFACT_FILTER_NAME
static java.lang.String	ALIGNMENT_SCORE_DIFFERENCE_KEY
static java.lang.String	ALLELE_BALANCE_HET_KEY
static java.lang.String	ALLELE_BALANCE_HOM_KEY
static java.lang.String	ALLELE_BALANCE_KEY
static java.lang.String	ALLELE_FRACTION_FILTER_NAME
static java.lang.String	ALLELE_FRACTION_KEY
static java.lang.String	ALLELE_SPECIFIC_ANNOTATION_PREFIX
static java.lang.String	ALLELE_SPECIFIC_PREFIX
static java.lang.String	ARTIFACT_IN_NORMAL_FILTER_NAME
static java.lang.String	AS_ALT_ALLELE_DEPTH_KEY
static java.lang.String	AS_BASE_QUAL_RANK_SUM_KEY
static java.lang.String	AS_CULPRIT_KEY
static java.lang.String	AS_FILTER_STATUS_KEY
static java.lang.String	AS_FISHER_STRAND_KEY
static java.lang.String	AS_HETEROZYGOSITY_KEY
static java.lang.String	AS_INBREEDING_COEFFICIENT_KEY
static java.lang.String	AS_MAP_QUAL_RANK_SUM_KEY
static java.lang.String	AS_QUAL_BY_DEPTH_KEY
static java.lang.String	AS_QUAL_KEY
static java.lang.String	AS_RAW_BASE_QUAL_RANK_SUM_KEY
static java.lang.String	AS_RAW_MAP_QUAL_RANK_SUM_KEY
static java.lang.String	AS_RAW_QUAL_APPROX_KEY
static java.lang.String	AS_RAW_READ_POS_RANK_SUM_KEY
static java.lang.String	AS_RAW_RMS_MAPPING_QUALITY_KEY
static java.lang.String	AS_READ_POS_RANK_SUM_KEY
static java.lang.String	AS_RMS_MAPPING_QUALITY_KEY
static java.lang.String	AS_SB_TABLE_KEY
static java.lang.String	AS_STRAND_ODDS_RATIO_KEY
static java.lang.String	AS_VARIANT_DEPTH_KEY
static java.lang.String	AS_VQS_LOD_KEY
static java.lang.String	ASSEMBLY_NAME_KEY
static java.lang.String	AVG_INTERVAL_DP_BY_SAMPLE_KEY
static java.lang.String	AVG_INTERVAL_DP_KEY
static java.lang.String	BAD_HAPLOTYPE_FILTER_NAME
static java.lang.String	BASE_COUNTS_KEY
static java.lang.String	BASE_QUAL_RANK_SUM_KEY
static java.lang.String	CHIMERIC_ORIGINAL_ALIGNMENT_FILTER_NAME
static java.lang.String	CLIPPING_RANK_SUM_KEY
static java.lang.String	CLUSTERED_EVENTS_FILTER_NAME
static java.lang.String	CNN_1D_KEY
static java.lang.String	CNN_2D_KEY
static java.lang.String	CONTAMINATION_FILTER_NAME
static java.lang.String	CONTAMINATION_QUAL_KEY
static java.lang.String	CONTIG_ID_KEY
static java.lang.String	CONTIG_LENGTH_KEY
static java.lang.String	CONVERTED_BASE_COVERAGE_KEY
static java.lang.String	CULPRIT_KEY
static java.lang.String	DOWNSAMPLED_KEY
static java.lang.String	DUPLICATED_EVIDENCE_FILTER_NAME
static java.lang.String	EVENT_COUNT_IN_HAPLOTYPE_KEY
static java.lang.String	EXCESS_HET_KEY
static java.lang.String	F1R2_KEY
static java.lang.String	F2R1_KEY
static java.lang.String	FISHER_STRAND_KEY
static java.lang.String	GC_CONTENT_KEY
static java.lang.String	GENOTYPE_AND_VALIDATE_STATUS_KEY
static java.lang.String	GENOTYPE_PRIOR_KEY
static java.lang.String	GENOTYPE_QUALITY_BY_ALLELE_BALANCE
static java.lang.String	GENOTYPE_QUALITY_BY_ALT_CONFIDENCE
static java.lang.String	GERMLINE_QUAL_KEY
static java.lang.String	GERMLINE_RISK_FILTER_NAME
static java.lang.String	GQ_MEAN_KEY
static java.lang.String	GQ_STDEV_KEY
static java.lang.String	HAPLOTYPE_CALLER_PHASING_GT_KEY
static java.lang.String	HAPLOTYPE_CALLER_PHASING_ID_KEY
static java.lang.String	HAPLOTYPE_SCORE_KEY
static java.lang.String	HARDY_WEINBERG_KEY
static java.lang.String	HI_CONF_DENOVO_KEY
static java.lang.String	HOMOPOLYMER_RUN_KEY
static java.lang.String	IN_PON_KEY
static java.lang.String	INBREEDING_COEFFICIENT_KEY
static java.lang.String	INTERVAL_GC_CONTENT_KEY
static java.lang.String	JOINT_ALIGNMENT_COUNT_KEY
static java.lang.String	JOINT_LIKELIHOOD_TAG_NAME
static java.lang.String	JOINT_POSTERIOR_TAG_NAME
static java.lang.String	LIKELIHOOD_RANK_SUM_KEY
static java.lang.String	LO_CONF_DENOVO_KEY
static java.lang.String	LOW_COVERAGE_LOCI
static java.lang.String	LOW_MQ_KEY
static java.lang.String	LOW_QUAL_FILTER_NAME
static java.lang.String	MAP_QUAL_RANK_SUM_KEY
static java.lang.String	MAPPING_QUALITY_DEPTH_DEPRECATED
static java.lang.String	MAPPING_QUALITY_ZERO_BY_SAMPLE_KEY
static java.lang.String	MEDIAN_BASE_QUALITY_FILTER_NAME
static java.lang.String	MEDIAN_BASE_QUALITY_KEY
static java.lang.String	MEDIAN_FRAGMENT_LENGTH_DIFFERENCE_FILTER_NAME
static java.lang.String	MEDIAN_FRAGMENT_LENGTH_KEY
static java.lang.String	MEDIAN_MAPPING_QUALITY_FILTER_NAME
static java.lang.String	MEDIAN_MAPPING_QUALITY_KEY
static java.lang.String	MEDIAN_READ_POSITON_KEY
static java.lang.String	MENDEL_VIOLATION_LR_KEY
static java.lang.String	METHYLATION_REFERENCE_CONTEXT_KEY
static java.lang.String	MIN_DP_FORMAT_KEY
static java.lang.String	MLE_ALLELE_COUNT_KEY
static java.lang.String	MLE_ALLELE_FREQUENCY_KEY
static java.lang.String	MLE_PER_SAMPLE_ALLELE_COUNT_KEY
static java.lang.String	MLE_PER_SAMPLE_ALLELE_FRACTION_KEY
static java.lang.String	MULTIALLELIC_FILTER_NAME
static java.util.List<java.lang.String>	MUTECT_FILTER_NAMES
static java.lang.String	N_COUNT_KEY
static java.lang.String	N_RATIO_FILTER_NAME
static java.lang.String	NEGATIVE_LABEL_KEY
static java.lang.String	NOCALL_CHROM_KEY
static java.lang.String	NON_DIPLOID_RATIO_KEY
static java.lang.String	NON_REF_SYMBOLIC_ALLELE_NAME
static java.lang.String	NORMAL_ARTIFACT_LOG_10_ODDS_KEY
static java.lang.String	NORMAL_LOG_10_ODDS_KEY
static java.lang.String	NUMBER_OF_DISCOVERED_ALLELES_KEY
static java.lang.String	ORIGINAL_AC_KEY
static java.lang.String	ORIGINAL_AF_KEY
static java.lang.String	ORIGINAL_AN_KEY
static java.lang.String	ORIGINAL_CONTIG_KEY
static java.lang.String	ORIGINAL_CONTIG_MISMATCH_KEY
static java.lang.String	ORIGINAL_DP_KEY
static java.lang.String	ORIGINAL_START_KEY
static java.lang.String	PHRED_SCALED_POSTERIORS_KEY
static java.lang.String	PL_FOR_ALL_SNP_ALLELES_KEY
static java.lang.String	POLYMERASE_SLIPPAGE
static java.lang.String	POLYMERASE_SLIPPAGE_QUAL_KEY
static java.lang.String	PON_FILTER_NAME
static java.lang.String	POPULATION_AF_KEY
static java.lang.String	POSITIVE_LABEL_KEY
static java.lang.String	POTENTIAL_POLYMORPHIC_NUMT_FILTER_NAME
static java.lang.String	QUAL_BY_DEPTH_KEY
static java.lang.String	RAW_GENOTYPE_COUNT_KEY
static java.lang.String	RAW_MAP_QUAL_RANK_SUM_KEY
static java.lang.String	RAW_MAPPING_QUALITY_WITH_DEPTH_KEY
static java.lang.String	RAW_QUAL_APPROX_KEY
static java.lang.String	RAW_RMS_MAPPING_QUALITY_DEPRECATED
static java.lang.String	RBP_HAPLOTYPE_KEY
static java.lang.String	RBP_INCONSISTENT_KEY
static java.lang.String	READ_ORIENTATION_ARTIFACT_FILTER_NAME
static java.lang.String	READ_ORIENTATION_QUAL_KEY
static java.lang.String	READ_POS_RANK_SUM_KEY
static java.lang.String	READ_POSITION_FILTER_NAME
static java.lang.String	REFERENCE_GENOTYPE_QUALITY
static java.lang.String	REFSAMPLE_DEPTH_KEY
static java.lang.String	REPEAT_UNIT_KEY
static java.lang.String	REPEATS_PER_ALLELE_KEY
static java.lang.String	SAMPLE_LIST_KEY
static java.lang.String	SB_TABLE_KEY
static java.lang.String	SEQUENCING_QUAL_KEY
static htsjdk.variant.variantcontext.Allele	SPANNING_DELETION_SYMBOLIC_ALLELE_DEPRECATED
static java.lang.String	SPANNING_DELETION_SYMBOLIC_ALLELE_NAME_DEPRECATED
static java.lang.String	SPANNING_DELETIONS_KEY
static java.lang.String	STR_PRESENT_KEY
static java.lang.String	STRAND_ARTIFACT_FILTER_NAME
static java.lang.String	STRAND_BIAS_BY_SAMPLE_KEY
static java.lang.String	STRAND_COUNT_BY_SAMPLE_KEY
static java.lang.String	STRAND_ODDS_RATIO_KEY
static java.lang.String	STRAND_QUAL_KEY
static java.lang.String	STRICT_STRAND_BIAS_FILTER_NAME
static java.lang.String	SYMBOLIC_ALLELE_DEFINITION_HEADER_TAG
static java.lang.String	TRANSMISSION_DISEQUILIBRIUM_KEY
static java.lang.String	TRANSMISSION_PROBABILITY_KEY
static java.lang.String	TUMOR_EVIDENCE_FILTER_NAME
static java.lang.String	TUMOR_LOG_10_ODDS_KEY
static java.lang.String	UNCONVERTED_BASE_COVERAGE_KEY
static java.lang.String	UNIQUE_ALT_READ_SET_COUNT_KEY
static java.lang.String	UNITIG_SIZES_KEY
static java.lang.String	VARIANT_DEPTH_KEY
static java.lang.String	VARIANT_TYPE_KEY
static java.lang.String	VQS_LOD_KEY
static java.lang.String	ZERO_COVERAGE_LOCI

Constructor Summary

Constructors

Constructor and Description
GATKVCFConstants()

Method Summary

Modifier and Type	Method and Description
static boolean	isSpanningDeletion(htsjdk.variant.variantcontext.Allele allele)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

CONTIG_ID_KEY

public static final java.lang.String CONTIG_ID_KEY

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Constant Field Values

CONTIG_LENGTH_KEY

public static final java.lang.String CONTIG_LENGTH_KEY

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Constant Field Values

ASSEMBLY_NAME_KEY

public static final java.lang.String ASSEMBLY_NAME_KEY

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Constant Field Values

ALLELE_SPECIFIC_PREFIX

public static final java.lang.String ALLELE_SPECIFIC_PREFIX

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Constant Field Values

AS_FILTER_STATUS_KEY

public static final java.lang.String AS_FILTER_STATUS_KEY

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Constant Field Values

RAW_RMS_MAPPING_QUALITY_DEPRECATED

public static final java.lang.String RAW_RMS_MAPPING_QUALITY_DEPRECATED

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Constant Field Values

MAPPING_QUALITY_DEPTH_DEPRECATED

public static final java.lang.String MAPPING_QUALITY_DEPTH_DEPRECATED

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Constant Field Values

RAW_MAPPING_QUALITY_WITH_DEPTH_KEY

public static final java.lang.String RAW_MAPPING_QUALITY_WITH_DEPTH_KEY

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Constant Field Values

AS_RMS_MAPPING_QUALITY_KEY

public static final java.lang.String AS_RMS_MAPPING_QUALITY_KEY

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Constant Field Values

AS_RAW_RMS_MAPPING_QUALITY_KEY

public static final java.lang.String AS_RAW_RMS_MAPPING_QUALITY_KEY

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Constant Field Values

AS_CULPRIT_KEY

public static final java.lang.String AS_CULPRIT_KEY

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Constant Field Values

AS_VQS_LOD_KEY

public static final java.lang.String AS_VQS_LOD_KEY

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Constant Field Values

ALLELE_BALANCE_HET_KEY

public static final java.lang.String ALLELE_BALANCE_HET_KEY

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Constant Field Values

ALLELE_BALANCE_HOM_KEY

public static final java.lang.String ALLELE_BALANCE_HOM_KEY

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Constant Field Values

ORIGINAL_AC_KEY

public static final java.lang.String ORIGINAL_AC_KEY

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Constant Field Values

ORIGINAL_AF_KEY

public static final java.lang.String ORIGINAL_AF_KEY

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Constant Field Values

ORIGINAL_AN_KEY

public static final java.lang.String ORIGINAL_AN_KEY

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Constant Field Values

AC_ADJUSTED_KEY

public static final java.lang.String AC_ADJUSTED_KEY

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Constant Field Values

BASE_COUNTS_KEY

public static final java.lang.String BASE_COUNTS_KEY

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Constant Field Values

BASE_QUAL_RANK_SUM_KEY

public static final java.lang.String BASE_QUAL_RANK_SUM_KEY

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Constant Field Values

AS_BASE_QUAL_RANK_SUM_KEY

public static final java.lang.String AS_BASE_QUAL_RANK_SUM_KEY

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Constant Field Values

AS_RAW_BASE_QUAL_RANK_SUM_KEY

public static final java.lang.String AS_RAW_BASE_QUAL_RANK_SUM_KEY

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Constant Field Values

GENOTYPE_AND_VALIDATE_STATUS_KEY

public static final java.lang.String GENOTYPE_AND_VALIDATE_STATUS_KEY

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Constant Field Values

CLIPPING_RANK_SUM_KEY

public static final java.lang.String CLIPPING_RANK_SUM_KEY

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Constant Field Values

CULPRIT_KEY

public static final java.lang.String CULPRIT_KEY

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Constant Field Values

SPANNING_DELETIONS_KEY

public static final java.lang.String SPANNING_DELETIONS_KEY

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Constant Field Values

ORIGINAL_DP_KEY

public static final java.lang.String ORIGINAL_DP_KEY

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Constant Field Values

DOWNSAMPLED_KEY

public static final java.lang.String DOWNSAMPLED_KEY

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Constant Field Values

EVENT_COUNT_IN_HAPLOTYPE_KEY

public static final java.lang.String EVENT_COUNT_IN_HAPLOTYPE_KEY

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Constant Field Values

FISHER_STRAND_KEY

public static final java.lang.String FISHER_STRAND_KEY

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Constant Field Values

AS_FISHER_STRAND_KEY

public static final java.lang.String AS_FISHER_STRAND_KEY

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Constant Field Values

AS_SB_TABLE_KEY

public static final java.lang.String AS_SB_TABLE_KEY

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Constant Field Values

SB_TABLE_KEY

public static final java.lang.String SB_TABLE_KEY

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Constant Field Values

GC_CONTENT_KEY

public static final java.lang.String GC_CONTENT_KEY

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Constant Field Values

GQ_MEAN_KEY

public static final java.lang.String GQ_MEAN_KEY

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Constant Field Values

GQ_STDEV_KEY

public static final java.lang.String GQ_STDEV_KEY

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Constant Field Values

HAPLOTYPE_SCORE_KEY

public static final java.lang.String HAPLOTYPE_SCORE_KEY

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Constant Field Values

HI_CONF_DENOVO_KEY

public static final java.lang.String HI_CONF_DENOVO_KEY

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Constant Field Values

HOMOPOLYMER_RUN_KEY

public static final java.lang.String HOMOPOLYMER_RUN_KEY

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Constant Field Values

HARDY_WEINBERG_KEY

public static final java.lang.String HARDY_WEINBERG_KEY

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Constant Field Values

AVG_INTERVAL_DP_KEY

public static final java.lang.String AVG_INTERVAL_DP_KEY

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Constant Field Values

INTERVAL_GC_CONTENT_KEY

public static final java.lang.String INTERVAL_GC_CONTENT_KEY

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Constant Field Values

INBREEDING_COEFFICIENT_KEY

public static final java.lang.String INBREEDING_COEFFICIENT_KEY

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Constant Field Values

AS_INBREEDING_COEFFICIENT_KEY

public static final java.lang.String AS_INBREEDING_COEFFICIENT_KEY

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Constant Field Values

EXCESS_HET_KEY

public static final java.lang.String EXCESS_HET_KEY

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Constant Field Values

RAW_GENOTYPE_COUNT_KEY

public static final java.lang.String RAW_GENOTYPE_COUNT_KEY

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Constant Field Values

AS_HETEROZYGOSITY_KEY

public static final java.lang.String AS_HETEROZYGOSITY_KEY

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Constant Field Values

LIKELIHOOD_RANK_SUM_KEY

public static final java.lang.String LIKELIHOOD_RANK_SUM_KEY

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Constant Field Values

LO_CONF_DENOVO_KEY

public static final java.lang.String LO_CONF_DENOVO_KEY

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Constant Field Values

LOW_MQ_KEY

public static final java.lang.String LOW_MQ_KEY

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Constant Field Values

MLE_ALLELE_COUNT_KEY

public static final java.lang.String MLE_ALLELE_COUNT_KEY

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Constant Field Values

MLE_ALLELE_FREQUENCY_KEY

public static final java.lang.String MLE_ALLELE_FREQUENCY_KEY

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Constant Field Values

MLE_PER_SAMPLE_ALLELE_COUNT_KEY

public static final java.lang.String MLE_PER_SAMPLE_ALLELE_COUNT_KEY

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Constant Field Values

MLE_PER_SAMPLE_ALLELE_FRACTION_KEY

public static final java.lang.String MLE_PER_SAMPLE_ALLELE_FRACTION_KEY

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Constant Field Values

MAP_QUAL_RANK_SUM_KEY

public static final java.lang.String MAP_QUAL_RANK_SUM_KEY

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Constant Field Values

RAW_MAP_QUAL_RANK_SUM_KEY

public static final java.lang.String RAW_MAP_QUAL_RANK_SUM_KEY

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Constant Field Values

AS_MAP_QUAL_RANK_SUM_KEY

public static final java.lang.String AS_MAP_QUAL_RANK_SUM_KEY

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Constant Field Values

AS_RAW_MAP_QUAL_RANK_SUM_KEY

public static final java.lang.String AS_RAW_MAP_QUAL_RANK_SUM_KEY

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Constant Field Values

MENDEL_VIOLATION_LR_KEY

public static final java.lang.String MENDEL_VIOLATION_LR_KEY

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Constant Field Values

NOCALL_CHROM_KEY

public static final java.lang.String NOCALL_CHROM_KEY

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Constant Field Values

NUMBER_OF_DISCOVERED_ALLELES_KEY

public static final java.lang.String NUMBER_OF_DISCOVERED_ALLELES_KEY

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Constant Field Values

NEGATIVE_LABEL_KEY

public static final java.lang.String NEGATIVE_LABEL_KEY

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Constant Field Values

NON_DIPLOID_RATIO_KEY

public static final java.lang.String NON_DIPLOID_RATIO_KEY

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Constant Field Values

ORIGINAL_CONTIG_KEY

public static final java.lang.String ORIGINAL_CONTIG_KEY

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Constant Field Values

ORIGINAL_START_KEY

public static final java.lang.String ORIGINAL_START_KEY

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Constant Field Values

RBP_INCONSISTENT_KEY

public static final java.lang.String RBP_INCONSISTENT_KEY

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Constant Field Values

GENOTYPE_PRIOR_KEY

public static final java.lang.String GENOTYPE_PRIOR_KEY

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Constant Field Values

POSITIVE_LABEL_KEY

public static final java.lang.String POSITIVE_LABEL_KEY

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Constant Field Values

QUAL_BY_DEPTH_KEY

public static final java.lang.String QUAL_BY_DEPTH_KEY

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Constant Field Values

AS_QUAL_BY_DEPTH_KEY

public static final java.lang.String AS_QUAL_BY_DEPTH_KEY

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Constant Field Values

AS_QUAL_KEY

public static final java.lang.String AS_QUAL_KEY

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Constant Field Values

RAW_QUAL_APPROX_KEY

public static final java.lang.String RAW_QUAL_APPROX_KEY

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Constant Field Values

AS_RAW_QUAL_APPROX_KEY

public static final java.lang.String AS_RAW_QUAL_APPROX_KEY

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Constant Field Values

VARIANT_DEPTH_KEY

public static final java.lang.String VARIANT_DEPTH_KEY

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Constant Field Values

AS_VARIANT_DEPTH_KEY

public static final java.lang.String AS_VARIANT_DEPTH_KEY

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Constant Field Values

AS_ALT_ALLELE_DEPTH_KEY

public static final java.lang.String AS_ALT_ALLELE_DEPTH_KEY

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Constant Field Values

READ_POS_RANK_SUM_KEY

public static final java.lang.String READ_POS_RANK_SUM_KEY

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Constant Field Values

AS_READ_POS_RANK_SUM_KEY

public static final java.lang.String AS_READ_POS_RANK_SUM_KEY

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Constant Field Values

AS_RAW_READ_POS_RANK_SUM_KEY

public static final java.lang.String AS_RAW_READ_POS_RANK_SUM_KEY

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Constant Field Values

REFSAMPLE_DEPTH_KEY

public static final java.lang.String REFSAMPLE_DEPTH_KEY

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Constant Field Values

REPEATS_PER_ALLELE_KEY

public static final java.lang.String REPEATS_PER_ALLELE_KEY

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Constant Field Values

REPEAT_UNIT_KEY

public static final java.lang.String REPEAT_UNIT_KEY

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Constant Field Values

SAMPLE_LIST_KEY

public static final java.lang.String SAMPLE_LIST_KEY

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Constant Field Values

STRAND_ODDS_RATIO_KEY

public static final java.lang.String STRAND_ODDS_RATIO_KEY

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Constant Field Values

AS_STRAND_ODDS_RATIO_KEY

public static final java.lang.String AS_STRAND_ODDS_RATIO_KEY

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Constant Field Values

STR_PRESENT_KEY

public static final java.lang.String STR_PRESENT_KEY

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Constant Field Values

TRANSMISSION_DISEQUILIBRIUM_KEY

public static final java.lang.String TRANSMISSION_DISEQUILIBRIUM_KEY

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Constant Field Values

VARIANT_TYPE_KEY

public static final java.lang.String VARIANT_TYPE_KEY

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Constant Field Values

VQS_LOD_KEY

public static final java.lang.String VQS_LOD_KEY

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Constant Field Values

CNN_1D_KEY

public static final java.lang.String CNN_1D_KEY

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Constant Field Values

CNN_2D_KEY

public static final java.lang.String CNN_2D_KEY

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Constant Field Values

F1R2_KEY

public static final java.lang.String F1R2_KEY

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Constant Field Values

F2R1_KEY

public static final java.lang.String F2R1_KEY

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Constant Field Values

TUMOR_LOG_10_ODDS_KEY

public static final java.lang.String TUMOR_LOG_10_ODDS_KEY

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Constant Field Values

NORMAL_LOG_10_ODDS_KEY

public static final java.lang.String NORMAL_LOG_10_ODDS_KEY

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Constant Field Values

IN_PON_KEY

public static final java.lang.String IN_PON_KEY

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Constant Field Values

NORMAL_ARTIFACT_LOG_10_ODDS_KEY

public static final java.lang.String NORMAL_ARTIFACT_LOG_10_ODDS_KEY

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Constant Field Values

POPULATION_AF_KEY

public static final java.lang.String POPULATION_AF_KEY

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Constant Field Values

GERMLINE_QUAL_KEY

public static final java.lang.String GERMLINE_QUAL_KEY

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Constant Field Values

SEQUENCING_QUAL_KEY

public static final java.lang.String SEQUENCING_QUAL_KEY

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Constant Field Values

POLYMERASE_SLIPPAGE_QUAL_KEY

public static final java.lang.String POLYMERASE_SLIPPAGE_QUAL_KEY

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Constant Field Values

STRAND_QUAL_KEY

public static final java.lang.String STRAND_QUAL_KEY

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Constant Field Values

CONTAMINATION_QUAL_KEY

public static final java.lang.String CONTAMINATION_QUAL_KEY

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Constant Field Values

READ_ORIENTATION_QUAL_KEY

public static final java.lang.String READ_ORIENTATION_QUAL_KEY

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Constant Field Values

ORIGINAL_CONTIG_MISMATCH_KEY

public static final java.lang.String ORIGINAL_CONTIG_MISMATCH_KEY

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Constant Field Values

N_COUNT_KEY

public static final java.lang.String N_COUNT_KEY

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Constant Field Values

UNIQUE_ALT_READ_SET_COUNT_KEY

public static final java.lang.String UNIQUE_ALT_READ_SET_COUNT_KEY

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Constant Field Values

MEDIAN_BASE_QUALITY_KEY

public static final java.lang.String MEDIAN_BASE_QUALITY_KEY

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Constant Field Values

MEDIAN_MAPPING_QUALITY_KEY

public static final java.lang.String MEDIAN_MAPPING_QUALITY_KEY

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Constant Field Values

MEDIAN_FRAGMENT_LENGTH_KEY

public static final java.lang.String MEDIAN_FRAGMENT_LENGTH_KEY

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Constant Field Values

MEDIAN_READ_POSITON_KEY

public static final java.lang.String MEDIAN_READ_POSITON_KEY

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Constant Field Values

UNITIG_SIZES_KEY

public static final java.lang.String UNITIG_SIZES_KEY

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Constant Field Values

ALIGNMENT_SCORE_DIFFERENCE_KEY

public static final java.lang.String ALIGNMENT_SCORE_DIFFERENCE_KEY

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Constant Field Values

JOINT_ALIGNMENT_COUNT_KEY

public static final java.lang.String JOINT_ALIGNMENT_COUNT_KEY

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Constant Field Values

UNCONVERTED_BASE_COVERAGE_KEY

public static final java.lang.String UNCONVERTED_BASE_COVERAGE_KEY

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Constant Field Values

CONVERTED_BASE_COVERAGE_KEY

public static final java.lang.String CONVERTED_BASE_COVERAGE_KEY

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Constant Field Values

METHYLATION_REFERENCE_CONTEXT_KEY

public static final java.lang.String METHYLATION_REFERENCE_CONTEXT_KEY

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Constant Field Values

ALLELE_BALANCE_KEY

public static final java.lang.String ALLELE_BALANCE_KEY

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Constant Field Values

PL_FOR_ALL_SNP_ALLELES_KEY

public static final java.lang.String PL_FOR_ALL_SNP_ALLELES_KEY

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Constant Field Values

RBP_HAPLOTYPE_KEY

public static final java.lang.String RBP_HAPLOTYPE_KEY

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Constant Field Values

AVG_INTERVAL_DP_BY_SAMPLE_KEY

public static final java.lang.String AVG_INTERVAL_DP_BY_SAMPLE_KEY

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Constant Field Values

JOINT_LIKELIHOOD_TAG_NAME

public static final java.lang.String JOINT_LIKELIHOOD_TAG_NAME

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Constant Field Values

JOINT_POSTERIOR_TAG_NAME

public static final java.lang.String JOINT_POSTERIOR_TAG_NAME

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Constant Field Values

LOW_COVERAGE_LOCI

public static final java.lang.String LOW_COVERAGE_LOCI

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Constant Field Values

MIN_DP_FORMAT_KEY

public static final java.lang.String MIN_DP_FORMAT_KEY

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Constant Field Values

MAPPING_QUALITY_ZERO_BY_SAMPLE_KEY

public static final java.lang.String MAPPING_QUALITY_ZERO_BY_SAMPLE_KEY

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Constant Field Values

HAPLOTYPE_CALLER_PHASING_GT_KEY

public static final java.lang.String HAPLOTYPE_CALLER_PHASING_GT_KEY

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Constant Field Values

HAPLOTYPE_CALLER_PHASING_ID_KEY

public static final java.lang.String HAPLOTYPE_CALLER_PHASING_ID_KEY

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Constant Field Values

PHRED_SCALED_POSTERIORS_KEY

public static final java.lang.String PHRED_SCALED_POSTERIORS_KEY

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Constant Field Values

REFERENCE_GENOTYPE_QUALITY

public static final java.lang.String REFERENCE_GENOTYPE_QUALITY

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Constant Field Values

GENOTYPE_QUALITY_BY_ALLELE_BALANCE

public static final java.lang.String GENOTYPE_QUALITY_BY_ALLELE_BALANCE

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Constant Field Values

GENOTYPE_QUALITY_BY_ALT_CONFIDENCE

public static final java.lang.String GENOTYPE_QUALITY_BY_ALT_CONFIDENCE

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Constant Field Values

STRAND_COUNT_BY_SAMPLE_KEY

public static final java.lang.String STRAND_COUNT_BY_SAMPLE_KEY

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Constant Field Values

STRAND_BIAS_BY_SAMPLE_KEY

public static final java.lang.String STRAND_BIAS_BY_SAMPLE_KEY

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Constant Field Values

TRANSMISSION_PROBABILITY_KEY

public static final java.lang.String TRANSMISSION_PROBABILITY_KEY

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Constant Field Values

ZERO_COVERAGE_LOCI

public static final java.lang.String ZERO_COVERAGE_LOCI

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Constant Field Values

ALLELE_FRACTION_KEY

public static final java.lang.String ALLELE_FRACTION_KEY

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Constant Field Values

CLUSTERED_EVENTS_FILTER_NAME

public static final java.lang.String CLUSTERED_EVENTS_FILTER_NAME

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Constant Field Values

GERMLINE_RISK_FILTER_NAME

public static final java.lang.String GERMLINE_RISK_FILTER_NAME

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Constant Field Values

LOW_QUAL_FILTER_NAME

public static final java.lang.String LOW_QUAL_FILTER_NAME

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Constant Field Values

ALIGNMENT_ARTIFACT_FILTER_NAME

public static final java.lang.String ALIGNMENT_ARTIFACT_FILTER_NAME

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Constant Field Values

PON_FILTER_NAME

public static final java.lang.String PON_FILTER_NAME

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Constant Field Values

POLYMERASE_SLIPPAGE

public static final java.lang.String POLYMERASE_SLIPPAGE

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Constant Field Values

TUMOR_EVIDENCE_FILTER_NAME

public static final java.lang.String TUMOR_EVIDENCE_FILTER_NAME

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Constant Field Values

MULTIALLELIC_FILTER_NAME

public static final java.lang.String MULTIALLELIC_FILTER_NAME

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Constant Field Values

STRAND_ARTIFACT_FILTER_NAME

public static final java.lang.String STRAND_ARTIFACT_FILTER_NAME

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Constant Field Values

DUPLICATED_EVIDENCE_FILTER_NAME

public static final java.lang.String DUPLICATED_EVIDENCE_FILTER_NAME

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Constant Field Values

ARTIFACT_IN_NORMAL_FILTER_NAME

public static final java.lang.String ARTIFACT_IN_NORMAL_FILTER_NAME

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Constant Field Values

MEDIAN_BASE_QUALITY_FILTER_NAME

public static final java.lang.String MEDIAN_BASE_QUALITY_FILTER_NAME

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Constant Field Values

MEDIAN_MAPPING_QUALITY_FILTER_NAME

public static final java.lang.String MEDIAN_MAPPING_QUALITY_FILTER_NAME

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Constant Field Values

MEDIAN_FRAGMENT_LENGTH_DIFFERENCE_FILTER_NAME

public static final java.lang.String MEDIAN_FRAGMENT_LENGTH_DIFFERENCE_FILTER_NAME

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Constant Field Values

READ_POSITION_FILTER_NAME

public static final java.lang.String READ_POSITION_FILTER_NAME

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Constant Field Values

CONTAMINATION_FILTER_NAME

public static final java.lang.String CONTAMINATION_FILTER_NAME

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Constant Field Values

READ_ORIENTATION_ARTIFACT_FILTER_NAME

public static final java.lang.String READ_ORIENTATION_ARTIFACT_FILTER_NAME

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Constant Field Values

BAD_HAPLOTYPE_FILTER_NAME

public static final java.lang.String BAD_HAPLOTYPE_FILTER_NAME

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Constant Field Values

STRICT_STRAND_BIAS_FILTER_NAME

public static final java.lang.String STRICT_STRAND_BIAS_FILTER_NAME

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Constant Field Values

N_RATIO_FILTER_NAME

public static final java.lang.String N_RATIO_FILTER_NAME

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Constant Field Values

CHIMERIC_ORIGINAL_ALIGNMENT_FILTER_NAME

public static final java.lang.String CHIMERIC_ORIGINAL_ALIGNMENT_FILTER_NAME

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Constant Field Values

ALLELE_FRACTION_FILTER_NAME

public static final java.lang.String ALLELE_FRACTION_FILTER_NAME

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Constant Field Values

POTENTIAL_POLYMORPHIC_NUMT_FILTER_NAME

public static final java.lang.String POTENTIAL_POLYMORPHIC_NUMT_FILTER_NAME

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Constant Field Values

MUTECT_FILTER_NAMES

public static final java.util.List<java.lang.String> MUTECT_FILTER_NAMES

SYMBOLIC_ALLELE_DEFINITION_HEADER_TAG

public static final java.lang.String SYMBOLIC_ALLELE_DEFINITION_HEADER_TAG

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Constant Field Values

NON_REF_SYMBOLIC_ALLELE_NAME

public static final java.lang.String NON_REF_SYMBOLIC_ALLELE_NAME

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Constant Field Values

SPANNING_DELETION_SYMBOLIC_ALLELE_NAME_DEPRECATED

public static final java.lang.String SPANNING_DELETION_SYMBOLIC_ALLELE_NAME_DEPRECATED

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Constant Field Values

SPANNING_DELETION_SYMBOLIC_ALLELE_DEPRECATED

public static final htsjdk.variant.variantcontext.Allele SPANNING_DELETION_SYMBOLIC_ALLELE_DEPRECATED

ALLELE_SPECIFIC_ANNOTATION_PREFIX

public static final java.lang.String ALLELE_SPECIFIC_ANNOTATION_PREFIX

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Constant Field Values

Constructor Detail

GATKVCFConstants

public GATKVCFConstants()

Method Detail

isSpanningDeletion

public static boolean isSpanningDeletion(htsjdk.variant.variantcontext.Allele allele)