VCFProcessor Logo
  • Overview
    • Introduction
    • Principle
      • Functions
      • Filters
  • Functions
    • General Information
      • Optional Arguments for all Functions
    • VCF Filter Functions
      • CompoundHeterozygous
      • DeNovo
      • DeNovoRecessive
      • Dominant
      • FilterConsequenceLevel
      • FilterF2
      • FilterFrequencies
      • FilterGeneCsqLevel
      • FilterGeneCsqList
      • FilterGenotype
      • FilterGnomADFrequency
      • FilterGnomADNFEFrequency
      • FilterKnownID
      • FilterNew
      • FoundInAllCases
      • HQ
      • KeepHomoAlt
      • MergeVQSR
      • MonoAllelicSNV
      • NotFoundInAnyControl
      • QC
      • RandomVariants
      • Recessive
      • Recode
      • RemoveNonSNV
      • RemoveNonVariant
      • SplitByChromosome
      • SplitByGene
      • SplitFromDB
      • StrictCompoundHeterozygous
    • VCF Transformation Functions
      • ClearInfoField
      • FilterCsqExtractGene
      • GenerateHomoRefForPosition
      • MissingToMajor
      • MissingToRef
      • Scramble
      • SetGenotypeFromProbability
      • SimulateVCFFromExisting
      • SplitMultiAllelic
      • VCFToReference
    • VCF Annotation Functions
      • AddAlleleBalance
      • AddDbSNP
      • AddGroupACANAF
      • AddWorstAndCanonicalConsequence
      • ReaffectdbSNP
      • UpdateACANAF
    • Analysis Functions
      • CheckReference
      • Chi2
      • CommonVariants
      • CompareGenotype
      • CompareToGnomAD
      • CountFromPublicDB
      • CountGenotypes
      • CountMissing
      • CountVariants
      • CountVariantsFoundIn
      • DbSNPMismatch
      • ExtractAlleleCounts
      • ExtractCanonical
      • ExtractNeighbours
      • ExtractPrivateToGroup
      • F2
      • F2Individuals
      • FrequencyCorrelation
      • FrequencyForPrivate
      • GeneList
      • GetQCMetrics
      • GetWorstConsequence
      • InbreedingCoeffDistribution
      • IQSBySample
      • IQSByVariant
      • JFSSummary
      • JointFrequencySpectrum
      • Kappa
      • MaleFemale
      • MeanQuality
      • MultiAllelicProportion
      • NumberOfCsqPerGene
      • NumberOfLinesFromTabix
      • PrivateAndShared
      • PrivateVSPanel
      • QCParametersDistribution
      • SampleStats
      • SharedAlleleMatrix
      • VQSLod
    • Formatting Functions
      • ShowFields
      • TSV2HTML
      • VCF2HTML
      • VCF2TSV
      • VCF2TSVGeneCsq
    • Other Functions
      • CoverageStats
      • ExtendBed
      • GeneCards
      • GeneCardsParser
      • GzPaste
      • IsInBed
      • NormalizePed
      • RandomPed
      • SimplifyBED
    • Graphics
      • GraphCompareFrequencies
      • GraphCountGenotypes
      • GraphF2
      • GraphJFS
      • GraphSampleStats
  • Filters
    • Position Filters
      • keep-pos
      • keep-positions
      • keep-bed
      • keep-pos-overlap
      • keep-positions-overlap
      • remove-pos
      • remove-positions
      • remove-bed
      • remove-pos-overlap
      • remove-positions-overlap
      • thin
    • Sample Filters
      • keep-sample
      • remove-sample
      • keep-samples
      • remove-samples
      • max-sample
      • ped
      • keep-family
      • remove-family
      • keep-sex
      • remove-sex
      • keep-phenotype
      • remove-phenotype
      • keep-group
      • remove-group
    • Genotype Filters
      • remove-filtered-geno-all
      • keep-filtered-geno
      • remove-filtered-geno
      • minDP
      • maxDP
      • minGQ
      • maxGQ
      • minVAF
      • maxVAF
      • abhetdev
    • Variant Frequency Filters
      • min-maf
      • max-maf
      • min-group-maf
      • max-group-maf
      • min-ref-af
      • max-ref-af
      • min-group-ref-af
      • max-group-ref-af
      • min-all-non-ref-af
      • max-all-non-ref-af
      • min-group-all-non-ref-af
      • max-group-all-non-ref-af
      • min-any-non-ref-af
      • max-any-non-ref-af
      • min-group-any-non-ref-af
      • max-group-any-non-ref-af
      • min-ref-ac
      • max-ref-ac
      • min-group-ref-ac
      • max-group-ref-ac
      • min-all-non-ref-ac
      • max-all-non-ref-ac
      • min-group-all-non-ref-ac
      • max-group-all-non-ref-ac
      • min-mac
      • max-mac
      • min-group-mac
      • max-group-mac
      • min-any-non-ref-ac
      • max-any-non-ref-ac
      • min-group-any-non-ref-ac
      • max-group-any-non-ref-ac
    • Variant Property Filters
      • keep-id
      • remove-id
      • keep-ids
      • remove-ids
      • keep-indels
      • remove-indels
      • keep-snvs
      • remove-snvs
      • keep-filtered-all
      • keep-filtered-any
      • remove-filtered-all
      • remove-filtered-any
      • strict-keep-filtered-all
      • strict-keep-filtered-any
      • strict-remove-filtered-all
      • strict-remove-filtered-any
      • keep-any-info
      • keep-all-info
      • remove-any-info
      • remove-all-info
      • min-alleles
      • max-alleles
      • min-meanDP
      • min-medianDP
      • max-meanDP
      • max-medianDP
      • min-meanGQ
      • min-medianGQ
      • max-meanGQ
      • max-medianGQ
      • hwe
      • remove-hwe
      • max-missing
      • min-missing
      • max-missing-count
      • min-missing-count
      • phased
      • remove-phased
      • minQ
      • maxQ
  • File Formats
    • VCF v4.2
    • PED
    • BED
  • Download
  • Changelog
    • 1.1.0 (2024-05-16)
      • core
      • functions
      • filters
    • 1.0.5 (2023-07-13)
      • core
      • functions
      • filters
    • 1.0.4 (2022-08-04)
      • core
      • functions
      • filters
    • 1.0.3 (2020-12-09)
      • core
      • functions
      • filters
      • other
    • 1.0.2 (2020-11-05)
      • core
      • functions
      • filters
      • other
    • 1.0.1 (2020-09-30)
      • core
      • functions
      • filters
      • other
    • 1.0.0 (2020-09-24)
      • core
      • functions
      • filters
      • other
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© Copyright 2020, Thomas E. Ludwig.

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