VCFProcessor
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
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
SplitMultiAllelic
VCFToReference
VCF Annotation Functions
AddAlleleBalance
AddDbSNP
AddGroupACANAF
AddWorstAndCanonicalConsequence
ReaffectdbSNP
UpdateACANAF
Analysis Functions
CheckReference
Chi2
CommonVariants
CompareGenotype
CompareToGnomAD
CountFromPublicDB
CountGenotypes
CountMissing
CountVariants
DbSNPMismatch
ExtractAlleleCounts
ExtractNeighbours
ExtractPrivateToGroup
F2
F2Individuals
FrequencyCorrelation
FrequencyForPrivate
GeneList
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
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
Graphical User Interface
Download
Changelog
1.0.4 (2020-12-16)
core
functions
filters
other
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
VCFProcessor
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Graphical User Interface
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Graphical User Interface
ΒΆ
VCFProcessor can be run in a graphical mode.