public class JannovarAnnotateVCFOptions extends JannovarAnnotationOptions
Modifier and Type | Class and Description |
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static class |
JannovarAnnotateVCFOptions.BedAnnotationOptions
Configuration for annotation with BED file.
|
Modifier and Type | Field and Description |
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boolean |
annotateAsSingletonPedigree
Whether or not to perform compatible inheritance mode annotation with the assumption that the single individual
is the affected index.
|
String |
pathClinVar
Path to ClinVar VCF file to use for the annotation
|
String |
pathCosmic
Path to COSMIC VCF file to use for the annotation
|
String |
pathFASTARef
Path to the reference FAI-indexed FASTA file (required for dbSNP/ExAC/UK10K-based annotation
|
String |
pathPedFile
Path to pedigree file
|
String |
pathThousandGenomes
Path to thousand genomes VCF file to use for the annotation
|
String |
pathVCFDBSNP
Path to dbSNP VCF file to use for the annotation
|
String |
pathVCFExac
Path to ExAC VCF file to use for the annotation
|
String |
pathVCFGnomadExomes
Path to gnomAD exomes VCF file to use for the annotation
|
String |
pathVCFGnomadGenomes
Path to gnomAD genomes VCF file to use for the annotation
|
String |
pathVCFUK10K
Path to UK10K VCF file to use for the annotation
|
String |
prefixClinVar
Prefix to use for ClinVar VCF INFO Fields
|
String |
prefixCosmic
Prefix to use for COSMIC VCF INFO Fields
|
String |
prefixDBSNP
Prefix to use for dbSNP VCF INFO Fields
|
String |
prefixExac
Prefix to use for ExAC VCF INFO Fields
|
String |
prefixGnomadExomes
Prefix to use for gnomAD exomes INFO fields
|
String |
prefixGnomadGenomes
Prefix to use for gnomAD genomes INFO fields
|
String |
prefixThousandGenomes
Prefix to use for thousand genomes VCF INFO Fields
|
String |
prefixUK10K
Prefix to use for UK10K VCF INFO Fields
|
boolean |
useAdvancedPedigreeFilters
Whether or not to use the advanced pedigree filters (mainly useful for de novo variants)
|
boolean |
useThresholdFilters
Whether or not to use threshold-based filters
|
Constructor and Description |
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JannovarAnnotateVCFOptions() |
getDatabaseFilePath, isNt3PrimeShifting, isShowAll, isUseThreeLetterAminoAcidCode, setDatabaseFilePath, setNt3PrimeShifting, setShowAll, setupParser, setUseThreeLetterAminoAcidCode
getFtpProxy, getHttpProxy, getHttpsProxy, getVerbosity, isReportProgress, setFtpProxy, setHttpProxy, setHttpsProxy, setReportProgress, setVerbosity
public String pathVCFDBSNP
public String prefixDBSNP
public String pathFASTARef
public String pathVCFExac
public String prefixExac
public String pathVCFGnomadExomes
public String prefixGnomadExomes
public String pathVCFGnomadGenomes
public String prefixGnomadGenomes
public String pathVCFUK10K
public String prefixUK10K
public String pathThousandGenomes
public String prefixThousandGenomes
public String pathClinVar
public String prefixClinVar
public String pathCosmic
public String prefixCosmic
public String pathPedFile
public boolean annotateAsSingletonPedigree
public boolean useThresholdFilters
public boolean useAdvancedPedigreeFilters
public static void setupParser(net.sourceforge.argparse4j.inf.Subparsers subParsers)
ArgumentParser
subParsers
- Subparsers
to setuppublic void setFromArgs(net.sourceforge.argparse4j.inf.Namespace args) throws CommandLineParsingException
JannovarBaseOptions
Namespace
objectsetFromArgs
in class JannovarAnnotationOptions
args
- Namespace
to get the option values fromCommandLineParsingException
- on problems parsing a given URLpublic String getInterval()
public void setInterval(String interval)
public String getPathInputVCF()
public void setPathInputVCF(String pathInputVCF)
public String getPathOutputVCF()
public void setPathOutputVCF(String pathOutputVCF)
public boolean isEscapeAnnField()
public void setEscapeAnnField(boolean escapeAnnField)
public String getPathVCFDBSNP()
public void setPathVCFDBSNP(String pathVCFDBSNP)
public String getPrefixDBSNP()
public void setPrefixDBSNP(String prefixDBSNP)
public String getPathFASTARef()
public void setPathFASTARef(String pathFASTARef)
public String getPathVCFExac()
public void setPathVCFExac(String pathVCFExac)
public String getPrefixExac()
public void setPrefixExac(String prefixExac)
public String getPathVCFUK10K()
public void setPathVCFUK10K(String pathVCFUK10K)
public String getPrefixUK10K()
public void setPrefixUK10K(String prefixUK10K)
public String getPathClinVar()
public void setPathClinVar(String pathClinVar)
public String getPrefixClinVar()
public void setPrefixClinVar(String prefixClinVar)
public String getPathCosmic()
public void setPathCosmic(String pathCosmic)
public String getPrefixCosmic()
public void setPrefixCosmic(String prefixCosmic)
public String getPathVCFGnomadExomes()
public void setPathVCFGnomadExomes(String pathVCFGnomadExomes)
public String getPrefixGnomadExomes()
public void setPrefixGnomadExomes(String prefixGnomadExomes)
public String getPathVCFGnomadGenomes()
public void setPathVCFGnomadGenomes(String pathVCFGnomadGenomes)
public String getPrefixGnomadGenomes()
public void setPrefixGnomadGenomes(String prefixGnomadGenomes)
public boolean isAnnotateAsSingletonPedigree()
public void setAnnotateAsSingletonPedigree(boolean annotateAsSingletonPedigree)
public String getPathPedFile()
public void setPathPedFile(String pathPedFile)
public boolean isUseThresholdFilters()
public void setUseThresholdFilters(boolean useThresholdFilters)
public int getThreshFiltMinGtCovHet()
public void setThreshFiltMinGtCovHet(int threshFiltMinGtCovHet)
public int getThreshFiltMinGtCovHomAlt()
public void setThreshFiltMinGtCovHomAlt(int threshFiltMinGtCovHomAlt)
public int getThreshFiltMaxCov()
public void setThreshFiltMaxCov(int threshFiltMaxCov)
public int getThreshFiltMinGtGq()
public void setThreshFiltMinGtGq(int threshFiltMinGtGq)
public double getThreshFiltMinGtAafHet()
public void setThreshFiltMinGtAafHet(double threshFiltMinGtAafHet)
public double getThreshFiltMaxGtAafHet()
public void setThreshFiltMaxGtAafHet(double threshFiltMaxGtAafHet)
public double getThreshFiltMinGtAafHomAlt()
public void setThreshFiltMinGtAafHomAlt(double threshFiltMinGtAafHomAlt)
public double getThreshFiltMaxGtAafHomRef()
public void setThreshFiltMaxGtAafHomRef(double threshFiltMaxGtAafHomRef)
public double getThreshFiltMaxAlleleFrequencyAd()
public void setThreshFiltMaxAlleleFrequencyAd(double threshFiltMaxAlleleFrequencyAd)
public void setThreshFiltMaxAlleleFrequencyAD(double threshFiltMaxAlleleFrequencyAd)
public double getThreshFiltMaxAlleleFrequencyAr()
public void setThreshFiltMaxAlleleFrequencyAr(double threshFiltMaxAlleleFrequencyAr)
public void setThreshFiltMaxAlleleFrequencyAR(double threshFiltMaxAlleleFrequencyAr)
public boolean isOffTargetFilterEnabled()
public void setOffTargetFilterEnabled(boolean offTargetFilterEnabled)
public boolean isOffTargetFilterUtrIsOffTarget()
public void setOffTargetFilterUtrIsOffTarget(boolean offTargetFilterUtrIsOffTarget)
public boolean isOffTargetFilterIntronicSpliceIsOffTarget()
public void setOffTargetFilterIntronicSpliceIsOffTarget(boolean offTargetFilterIntronicSpliceIsOffTarget)
public boolean isOneParentGtFilteredFiltersAffected()
public void setOneParentGtFilteredFiltersAffected(boolean oneParentGtFilteredFiltersAffected)
public boolean isInheritanceAnnoUseFilters()
public void setInheritanceAnnoUseFilters(boolean inheritanceAnnoUseFilters)
public boolean isUseAdvancedPedigreeFilters()
public void setUseAdvancedPedigreeFilters(boolean useAdvancedPedigreeFilters)
public List<JannovarAnnotateVCFOptions.BedAnnotationOptions> getBedAnnotationOptions()
public void setBedAnnotationOptions(List<JannovarAnnotateVCFOptions.BedAnnotationOptions> bedAnnotationOptions)
public Integer getThreshDeNovoParentAd2()
public void setThreshDeNovoParentAd2(Integer threshDeNovoParentAd2)
public String getPrefixDbNsfp()
public void setPrefixDbNsfp(String prefixDbNsfp)
public String getPathDbNsfp()
public void setPathDbNsfp(String pathDbNsfp)
public List<GenericTSVAnnotationOptions> getTsvAnnotationOptions()
public void setTsvAnnotationOptions(List<GenericTSVAnnotationOptions> tsvAnnotationOptions)
public int getDbNsfpColContig()
public void setDbNsfpColContig(int dbNsfpColContig)
public int getDbNsfpColPosition()
public void setDbNsfpColPosition(int dbNsfpColPosition)
public List<GenericVCFAnnotationOptions> getVcfAnnotationOptions()
public void setVcfAnnotationOptions(List<GenericVCFAnnotationOptions> vcfAnnotationOptions)
public boolean isUseParentGtIsFiltered()
public void setUseParentGtIsFiltered(boolean useParentGtIsFiltered)
public String getPathThousandGenomes()
public void setPathThousandGenomes(String pathThousandGenomes)
public String getPrefixThousandGenomes()
public void setPrefixThousandGenomes(String prefixThousandGenomes)
public int getThreshFiltMaxExacHomAlt()
public void setThreshFiltMaxExacHomAlt(int threshFiltMaxExacHomAlt)
public int getThreshFiltMaxThousandGenomesHomAlt()
public void setThreshFiltMaxThousandGenomesHomAlt(int threshFiltMaxThousandGenomesHomAlt)
public String toString()
toString
in class JannovarAnnotationOptions
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