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jannovar-cli, 0.30
A B C D E F G H I J L M P R S T U V 

A

aaalt - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
aapos - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
aaref - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ALSPAC_AC - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ALSPAC_AF - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
alt - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
AltaiNeandertal - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
Ancestral_allele - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
annotateAsSingletonPedigree - Variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
Whether or not to perform compatible inheritance mode annotation with the assumption that the single individual is the affected index.
AnnotateCSVCommand - Class in de.charite.compbio.jannovar.cmd.annotate_csv
Allows the annotation of a CVF file.
AnnotateCSVCommand(Namespace) - Constructor for class de.charite.compbio.jannovar.cmd.annotate_csv.AnnotateCSVCommand
 
AnnotatePositionCommand - Class in de.charite.compbio.jannovar.cmd.annotate_pos
Allows the annotation of a single position.
AnnotatePositionCommand(String[], Namespace) - Constructor for class de.charite.compbio.jannovar.cmd.annotate_pos.AnnotatePositionCommand
 
annotateVariantContext(VariantContext) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.BedFileAnnotator
Annotate and build the variant
AnnotateVCFCommand - Class in de.charite.compbio.jannovar.cmd.annotate_vcf
Run annotation steps (read in VCF, write out VCF or Jannovar file format).
AnnotateVCFCommand(String[], Namespace) - Constructor for class de.charite.compbio.jannovar.cmd.annotate_vcf.AnnotateVCFCommand
 

B

BedAnnotationOptions(String, String, String) - Constructor for class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions.BedAnnotationOptions
 
BedAnnotationOptions(String, String, String, int) - Constructor for class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions.BedAnnotationOptions
 
BedFileAnnotator - Class in de.charite.compbio.jannovar.cmd.annotate_vcf
Perform annotation of VariantContexts using BED files.
BedFileAnnotator(JannovarAnnotateVCFOptions.BedAnnotationOptions) - Constructor for class de.charite.compbio.jannovar.cmd.annotate_vcf.BedFileAnnotator
 

C

CADD_phred - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
CADD_raw - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
CADD_raw_rankscore - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
cds_strand - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
clinvar_clnsig - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
clinvar_golden_starsInterpro_domain - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
clinvar_rs - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
clinvar_trait - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
close() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.BedFileAnnotator
 
codon_degeneracy - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
codonpos - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
CommandLineParsingException - Exception in de.charite.compbio.jannovar.cmd
Exception thrown on problems with the command line.
CommandLineParsingException() - Constructor for exception de.charite.compbio.jannovar.cmd.CommandLineParsingException
 
CommandLineParsingException(String) - Constructor for exception de.charite.compbio.jannovar.cmd.CommandLineParsingException
 
CommandLineParsingException(String, Throwable) - Constructor for exception de.charite.compbio.jannovar.cmd.CommandLineParsingException
 

D

DANN_rankscore - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
DANN_score - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
DatabaseListCommand - Class in de.charite.compbio.jannovar.cmd.db_list
 
DatabaseListCommand(String[], Namespace) - Constructor for class de.charite.compbio.jannovar.cmd.db_list.DatabaseListCommand
 
dataSourceFiles - Variable in class de.charite.compbio.jannovar.cmd.JannovarDBOptions
paths to INI files ot use for parsing
DBNSFP_FIELDS - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
DbNsfpFields - Class in de.charite.compbio.jannovar.cmd.annotate_vcf
Configuration for annotation with dbNSFP (v3.4).
DbNsfpFields() - Constructor for class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
de.charite.compbio.jannovar - package de.charite.compbio.jannovar
 
de.charite.compbio.jannovar.cmd - package de.charite.compbio.jannovar.cmd
 
de.charite.compbio.jannovar.cmd.annotate_csv - package de.charite.compbio.jannovar.cmd.annotate_csv
 
de.charite.compbio.jannovar.cmd.annotate_pos - package de.charite.compbio.jannovar.cmd.annotate_pos
 
de.charite.compbio.jannovar.cmd.annotate_vcf - package de.charite.compbio.jannovar.cmd.annotate_vcf
 
de.charite.compbio.jannovar.cmd.db_list - package de.charite.compbio.jannovar.cmd.db_list
 
de.charite.compbio.jannovar.cmd.download - package de.charite.compbio.jannovar.cmd.download
 
de.charite.compbio.jannovar.cmd.hgvs_to_vcf - package de.charite.compbio.jannovar.cmd.hgvs_to_vcf
 
de.charite.compbio.jannovar.cmd.statistics - package de.charite.compbio.jannovar.cmd.statistics
 
Denisova - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
DownloadCommand - Class in de.charite.compbio.jannovar.cmd.download
Implementation of download step in Jannovar.
DownloadCommand(String[], Namespace) - Constructor for class de.charite.compbio.jannovar.cmd.download.DownloadCommand
 

E

Eigen_coding_or_noncoding - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
Eigen_PC_phred - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
Eigen_PC_raw - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
Eigen_PC_raw_rankscore - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
Eigen_phred - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
Eigen_raw - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
Ensembl_geneid - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
Ensembl_proteinid - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
Ensembl_transcriptid - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ESP6500_AA_AC - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ESP6500_AA_AF - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ESP6500_EA_AC - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ESP6500_EA_AF - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ExAC_AC - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ExAC_Adj_AC - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ExAC_Adj_AF - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ExAC_AF - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ExAC_AFR_AC - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ExAC_AFR_AF - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ExAC_AMR_AC - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ExAC_AMR_AF - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ExAC_EAS_AC - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ExAC_EAS_AF - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ExAC_FIN_AC - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ExAC_FIN_AF - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ExAC_NFE_AC - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ExAC_NFE_AF - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ExAC_nonpsych_AC - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ExAC_nonpsych_Adj_AC - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ExAC_nonpsych_Adj_AF - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ExAC_nonpsych_AF - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ExAC_nonpsych_AFR_AC - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ExAC_nonpsych_AFR_AF - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ExAC_nonpsych_AMR_AC - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ExAC_nonpsych_AMR_AF - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ExAC_nonpsych_EAS_ACExAC_nonpsych_EAS_AF - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ExAC_nonpsych_FIN_AC - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ExAC_nonpsych_FIN_AF - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ExAC_nonpsych_NFE_AC - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ExAC_nonpsych_NFE_AF - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ExAC_nonpsych_SAS_AC - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ExAC_nonpsych_SAS_AF - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ExAC_nonTCGA_AC - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ExAC_nonTCGA_Adj_AC - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ExAC_nonTCGA_Adj_AF - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ExAC_nonTCGA_AF - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ExAC_nonTCGA_AFR_AC - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ExAC_nonTCGA_AFR_AF - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ExAC_nonTCGA_AMR_AC - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ExAC_nonTCGA_AMR_AF - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ExAC_nonTCGA_EAS_AC - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ExAC_nonTCGA_EAS_AF - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ExAC_nonTCGA_FIN_AC - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ExAC_nonTCGA_FIN_AF - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ExAC_nonTCGA_NFE_AC - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ExAC_nonTCGA_NFE_AF - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ExAC_nonTCGA_SAS_AC - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ExAC_nonTCGA_SAS_AF - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ExAC_SAS_AC - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
ExAC_SAS_AF - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
extendHeader(VCFHeader) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.BedFileAnnotator
Add header line describing the INFO field.

F

FATHMM_converted_rankscore - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
fathmm_MKL_coding_group - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
fathmm_MKL_coding_pred - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
fathmm_MKL_coding_rankscore - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
fathmm_MKL_coding_score - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
FATHMM_pred - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
FATHMM_score - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 

G

G1000_Gp3_AC - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
G1000_Gp3_AF - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
G1000_Gp3_AFR_AC - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
G1000_Gp3_AFR_AF - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
G1000_Gp3_AMR_AC - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
G1000_Gp3_AMR_AF - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
G1000_Gp3_EAS_AC - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
G1000_Gp3_EAS_AF - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
G1000_Gp3_EUR_AC - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
G1000_Gp3_EUR_AF - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
G1000_Gp3_SAS_AC - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
G1000_Gp3_SAS_AF - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
GatherStatisticsCommand - Class in de.charite.compbio.jannovar.cmd.statistics
Jannovar command for gathering statistics about variant effect distribution etc.
GatherStatisticsCommand(String[], Namespace) - Constructor for class de.charite.compbio.jannovar.cmd.statistics.GatherStatisticsCommand
 
genename - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
GenoCanyon_score - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
GenoCanyon_score_rankscore - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
GERPpp_NR - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
GERPpp_RS - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
GERPpp_RS_rankscore - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
getAlt() - Method in class de.charite.compbio.jannovar.cmd.annotate_csv.JannovarAnnotateCSVOptions
 
getBedAnnotationOptions() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
getChr() - Method in class de.charite.compbio.jannovar.cmd.annotate_csv.JannovarAnnotateCSVOptions
 
getColNo() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions.BedAnnotationOptions
 
getColumnsDbNsfp() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
getCsv() - Method in class de.charite.compbio.jannovar.cmd.annotate_csv.JannovarAnnotateCSVOptions
 
getDatabaseFilePath() - Method in class de.charite.compbio.jannovar.cmd.JannovarAnnotationOptions
 
getDatabaseFilePath() - Method in class de.charite.compbio.jannovar.cmd.statistics.JannovarGatherStatisticsOptions
 
getDatabaseNames() - Method in class de.charite.compbio.jannovar.cmd.download.JannovarDownloadOptions
 
getDataSourceFiles() - Method in class de.charite.compbio.jannovar.cmd.JannovarDBOptions
 
getDbNsfpColContig() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
getDbNsfpColPosition() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
getDescription() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions.BedAnnotationOptions
 
getDownloadDir() - Method in class de.charite.compbio.jannovar.cmd.download.JannovarDownloadOptions
 
getFormat() - Method in class de.charite.compbio.jannovar.cmd.annotate_csv.JannovarAnnotateCSVOptions
 
getFtpProxy() - Method in class de.charite.compbio.jannovar.cmd.JannovarBaseOptions
 
getGeneIdentifiers() - Method in class de.charite.compbio.jannovar.cmd.download.JannovarDownloadOptions
 
getGenomicChanges() - Method in class de.charite.compbio.jannovar.cmd.annotate_pos.JannovarAnnotatePosOptions
 
getHttpProxy() - Method in class de.charite.compbio.jannovar.cmd.JannovarBaseOptions
 
getHttpsProxy() - Method in class de.charite.compbio.jannovar.cmd.JannovarBaseOptions
 
getInfoField() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions.BedAnnotationOptions
 
getInterval() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
getOutputFile() - Method in class de.charite.compbio.jannovar.cmd.download.JannovarDownloadOptions
 
getPathBed() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions.BedAnnotationOptions
 
getPathClinVar() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
getPathCosmic() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
getPathDbNsfp() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
getPathFASTARef() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
getPathInputText() - Method in class de.charite.compbio.jannovar.cmd.hgvs_to_vcf.ProjectTranscriptToChromosomeOptions
 
getPathInputVCF() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
getPathInputVCF() - Method in class de.charite.compbio.jannovar.cmd.statistics.JannovarGatherStatisticsOptions
 
getPathOutputReport() - Method in class de.charite.compbio.jannovar.cmd.statistics.JannovarGatherStatisticsOptions
 
getPathOutputVCF() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
getPathOutputVCF() - Method in class de.charite.compbio.jannovar.cmd.hgvs_to_vcf.ProjectTranscriptToChromosomeOptions
 
getPathPedFile() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
getPathReferenceFASTA() - Method in class de.charite.compbio.jannovar.cmd.hgvs_to_vcf.ProjectTranscriptToChromosomeOptions
 
getPathThousandGenomes() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
getPathVCFDBSNP() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
getPathVCFExac() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
getPathVCFGnomadExomes() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
getPathVCFGnomadGenomes() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
getPathVCFUK10K() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
getPos() - Method in class de.charite.compbio.jannovar.cmd.annotate_csv.JannovarAnnotateCSVOptions
 
getPrefixClinVar() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
getPrefixCosmic() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
getPrefixDbNsfp() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
getPrefixDBSNP() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
getPrefixExac() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
getPrefixGnomadExomes() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
getPrefixGnomadGenomes() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
getPrefixThousandGenomes() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
getPrefixUK10K() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
getRef() - Method in class de.charite.compbio.jannovar.cmd.annotate_csv.JannovarAnnotateCSVOptions
 
getThreshDeNovoParentAd2() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
getThreshFiltMaxAlleleFrequencyAd() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
getThreshFiltMaxAlleleFrequencyAr() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
getThreshFiltMaxCov() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
getThreshFiltMaxExacHomAlt() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
getThreshFiltMaxGtAafHet() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
getThreshFiltMaxGtAafHomRef() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
getThreshFiltMaxThousandGenomesHomAlt() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
getThreshFiltMinGtAafHet() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
getThreshFiltMinGtAafHomAlt() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
getThreshFiltMinGtCovHet() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
getThreshFiltMinGtCovHomAlt() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
getThreshFiltMinGtGq() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
getTsvAnnotationOptions() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
getVcfAnnotationOptions() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
getVerbosity() - Method in class de.charite.compbio.jannovar.cmd.JannovarBaseOptions
 
getVersion() - Static method in class de.charite.compbio.jannovar.Jannovar
 
GM12878_confidence_value - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
GM12878_fitCons_score - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
GM12878_fitCons_score_rankscore - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
GTEx_V6_gene - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
GTEx_V6_tissue - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 

H

H1_hESC_confidence_value - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
H1_hESC_fitCons_score - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
H1_hESC_fitCons_score_rankscore - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
HelpRequestedException - Exception in de.charite.compbio.jannovar.cmd
Thrown when the user requests help.
HelpRequestedException() - Constructor for exception de.charite.compbio.jannovar.cmd.HelpRequestedException
 
HelpRequestedException(String) - Constructor for exception de.charite.compbio.jannovar.cmd.HelpRequestedException
 
HelpRequestedException(String, Throwable) - Constructor for exception de.charite.compbio.jannovar.cmd.HelpRequestedException
 
hg18_chr - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
hg18_pos - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
hg19_chr - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
hg19_pos - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
hg38_chr - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
hg38_pos - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
HUVEC_confidence_value - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
HUVEC_fitCons_score - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
HUVEC_fitCons_score_rankscore - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 

I

integrated_confidence_value - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
integrated_fitCons_score - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
integrated_fitCons_score_rankscore - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
isAnnotateAsSingletonPedigree() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
isEscapeAnnField() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
isHeader() - Method in class de.charite.compbio.jannovar.cmd.annotate_csv.JannovarAnnotateCSVOptions
 
isInheritanceAnnoUseFilters() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
isNt3PrimeShifting() - Method in class de.charite.compbio.jannovar.cmd.JannovarAnnotationOptions
 
isOffTargetFilterEnabled() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
isOffTargetFilterIntronicSpliceIsOffTarget() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
isOffTargetFilterUtrIsOffTarget() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
isOneParentGtFilteredFiltersAffected() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
isReportProgress() - Method in class de.charite.compbio.jannovar.cmd.JannovarBaseOptions
 
isShowAll() - Method in class de.charite.compbio.jannovar.cmd.JannovarAnnotationOptions
 
isUseAdvancedPedigreeFilters() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
isUseParentGtIsFiltered() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
isUseThreeLetterAminoAcidCode() - Method in class de.charite.compbio.jannovar.cmd.JannovarAnnotationOptions
 
isUseThresholdFilters() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 

J

Jannovar - Class in de.charite.compbio.jannovar
This is the driver class for a program called Jannovar.
Jannovar() - Constructor for class de.charite.compbio.jannovar.Jannovar
 
JannovarAnnotateCSVOptions - Class in de.charite.compbio.jannovar.cmd.annotate_csv
Options for the annotate-pos comman
JannovarAnnotateCSVOptions() - Constructor for class de.charite.compbio.jannovar.cmd.annotate_csv.JannovarAnnotateCSVOptions
 
JannovarAnnotatePosOptions - Class in de.charite.compbio.jannovar.cmd.annotate_pos
Options for the annotate-pos comman
JannovarAnnotatePosOptions() - Constructor for class de.charite.compbio.jannovar.cmd.annotate_pos.JannovarAnnotatePosOptions
 
JannovarAnnotateVCFOptions - Class in de.charite.compbio.jannovar.cmd.annotate_vcf
Options for annotating VCF files
JannovarAnnotateVCFOptions() - Constructor for class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
JannovarAnnotateVCFOptions.BedAnnotationOptions - Class in de.charite.compbio.jannovar.cmd.annotate_vcf
Configuration for annotation with BED file.
JannovarAnnotationCommand - Class in de.charite.compbio.jannovar.cmd
Base class for commands needing annotation data.
JannovarAnnotationCommand() - Constructor for class de.charite.compbio.jannovar.cmd.JannovarAnnotationCommand
 
JannovarAnnotationOptions - Class in de.charite.compbio.jannovar.cmd
Configuration for the annotation commands
JannovarAnnotationOptions() - Constructor for class de.charite.compbio.jannovar.cmd.JannovarAnnotationOptions
 
JannovarBaseOptions - Class in de.charite.compbio.jannovar.cmd
Base option class for global Jannovar options
JannovarBaseOptions() - Constructor for class de.charite.compbio.jannovar.cmd.JannovarBaseOptions
 
JannovarCommand - Class in de.charite.compbio.jannovar.cmd
Super class for all commands, i.e.
JannovarCommand() - Constructor for class de.charite.compbio.jannovar.cmd.JannovarCommand
 
JannovarDBListOptions - Class in de.charite.compbio.jannovar.cmd.db_list
Configuration for the db-list command
JannovarDBListOptions() - Constructor for class de.charite.compbio.jannovar.cmd.db_list.JannovarDBListOptions
 
JannovarDBOptions - Class in de.charite.compbio.jannovar.cmd
Configuration for database-related commands in Jannovar
JannovarDBOptions() - Constructor for class de.charite.compbio.jannovar.cmd.JannovarDBOptions
 
JannovarDownloadOptions - Class in de.charite.compbio.jannovar.cmd.download
Configuration for the download command
JannovarDownloadOptions() - Constructor for class de.charite.compbio.jannovar.cmd.download.JannovarDownloadOptions
 
JannovarGatherStatisticsOptions - Class in de.charite.compbio.jannovar.cmd.statistics
Configuration for the statistics command
JannovarGatherStatisticsOptions() - Constructor for class de.charite.compbio.jannovar.cmd.statistics.JannovarGatherStatisticsOptions
 

L

LRT_converted_rankscore - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
LRT_Omega - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
LRT_pred - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
LRT_score - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 

M

M_CAP_pred - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
M_CAP_rankscore - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
M_CAP_score - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
main(String[]) - Static method in class de.charite.compbio.jannovar.Jannovar
 
MetaLR_pred - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
MetaLR_rankscore - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
MetaLR_score - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
MetaSVM_pred - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
MetaSVM_rankscore - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
MetaSVM_score - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
MutationAssessor_pred - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
MutationAssessor_score - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
MutationAssessor_score_rankscore - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
MutationAssessor_UniprotID - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
MutationAssessor_variant - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
MutationTaster_AAE - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
MutationTaster_converted_rankscore - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
MutationTaster_model - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
MutationTaster_pred - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
MutationTaster_score - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
MutPred_AAchange - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
MutPred_protID - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
MutPred_rankscore - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
MutPred_score - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
MutPred_Top5features - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 

P

parseFrom(String) - Static method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions.BedAnnotationOptions
Construct new BED annotation from command line option value.
pathClinVar - Variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
Path to ClinVar VCF file to use for the annotation
pathCosmic - Variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
Path to COSMIC VCF file to use for the annotation
pathFASTARef - Variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
Path to the reference FAI-indexed FASTA file (required for dbSNP/ExAC/UK10K-based annotation
pathPedFile - Variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
Path to pedigree file
pathThousandGenomes - Variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
Path to thousand genomes VCF file to use for the annotation
pathVCFDBSNP - Variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
Path to dbSNP VCF file to use for the annotation
pathVCFExac - Variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
Path to ExAC VCF file to use for the annotation
pathVCFGnomadExomes - Variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
Path to gnomAD exomes VCF file to use for the annotation
pathVCFGnomadGenomes - Variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
Path to gnomAD genomes VCF file to use for the annotation
pathVCFUK10K - Variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
Path to UK10K VCF file to use for the annotation
phastCons100way_vertebrate - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
phastCons100way_vertebrate_rankscore - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
phastCons20way_mammalian - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
phastCons20way_mammalian_rankscore - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
phyloP100way_vertebrate - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
phyloP100way_vertebrate_rankscore - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
phyloP20way_mammalian - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
phyloP20way_mammalian_rankscore - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
Polyphen2_HDIV_pred - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
Polyphen2_HDIV_rankscore - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
Polyphen2_HDIV_score - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
Polyphen2_HVAR_pred - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
Polyphen2_HVAR_rankscore - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
Polyphen2_HVAR_score - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
prefixClinVar - Variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
Prefix to use for ClinVar VCF INFO Fields
prefixCosmic - Variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
Prefix to use for COSMIC VCF INFO Fields
prefixDBSNP - Variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
Prefix to use for dbSNP VCF INFO Fields
prefixExac - Variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
Prefix to use for ExAC VCF INFO Fields
prefixGnomadExomes - Variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
Prefix to use for gnomAD exomes INFO fields
prefixGnomadGenomes - Variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
Prefix to use for gnomAD genomes INFO fields
prefixThousandGenomes - Variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
Prefix to use for thousand genomes VCF INFO Fields
prefixUK10K - Variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
Prefix to use for UK10K VCF INFO Fields
ProjectTranscriptToChromosome - Class in de.charite.compbio.jannovar.cmd.hgvs_to_vcf
Project transcript to chromosomal changes
ProjectTranscriptToChromosome(Namespace) - Constructor for class de.charite.compbio.jannovar.cmd.hgvs_to_vcf.ProjectTranscriptToChromosome
 
ProjectTranscriptToChromosomeOptions - Class in de.charite.compbio.jannovar.cmd.hgvs_to_vcf
Projection from transcript-level to chromosome-level changes
ProjectTranscriptToChromosomeOptions() - Constructor for class de.charite.compbio.jannovar.cmd.hgvs_to_vcf.ProjectTranscriptToChromosomeOptions
 
PROVEAN_converted_rankscore - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
PROVEAN_pred - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
PROVEAN_score - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 

R

ref - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
refcodon - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
Reliability_index - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
REVEL_rankscore - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
REVEL_score - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
rs_dbSNP147 - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
run() - Method in class de.charite.compbio.jannovar.cmd.annotate_csv.AnnotateCSVCommand
This function will simply annotate a csv file where positions are set
run() - Method in class de.charite.compbio.jannovar.cmd.annotate_pos.AnnotatePositionCommand
This function will simply annotate given chromosomal position with HGVS compliant output.
run() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.AnnotateVCFCommand
This function inputs a VCF file, and prints the annotated version thereof to a file (name of the original file with the suffix .de.charite.compbio.jannovar).
run() - Method in class de.charite.compbio.jannovar.cmd.db_list.DatabaseListCommand
Perform the downloading.
run() - Method in class de.charite.compbio.jannovar.cmd.download.DownloadCommand
Perform the downloading.
run() - Method in class de.charite.compbio.jannovar.cmd.hgvs_to_vcf.ProjectTranscriptToChromosome
 
run() - Method in class de.charite.compbio.jannovar.cmd.JannovarCommand
Function for the execution of the command.
run() - Method in class de.charite.compbio.jannovar.cmd.statistics.GatherStatisticsCommand
Compute the statistics

S

setAnnotateAsSingletonPedigree(boolean) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setBedAnnotationOptions(List<JannovarAnnotateVCFOptions.BedAnnotationOptions>) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setColumnsDbNsfp(List<String>) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setDatabaseFilePath(String) - Method in class de.charite.compbio.jannovar.cmd.JannovarAnnotationOptions
 
setDatabaseFilePath(String) - Method in class de.charite.compbio.jannovar.cmd.statistics.JannovarGatherStatisticsOptions
 
setDatabaseNames(List<String>) - Method in class de.charite.compbio.jannovar.cmd.download.JannovarDownloadOptions
 
setDataSourceFiles(List<String>) - Method in class de.charite.compbio.jannovar.cmd.JannovarDBOptions
 
setDbNsfpColContig(int) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setDbNsfpColPosition(int) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setDownloadDir(String) - Method in class de.charite.compbio.jannovar.cmd.download.JannovarDownloadOptions
 
setEscapeAnnField(boolean) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setFromArgs(Namespace) - Method in class de.charite.compbio.jannovar.cmd.annotate_csv.JannovarAnnotateCSVOptions
 
setFromArgs(Namespace) - Method in class de.charite.compbio.jannovar.cmd.annotate_pos.JannovarAnnotatePosOptions
 
setFromArgs(Namespace) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setFromArgs(Namespace) - Method in class de.charite.compbio.jannovar.cmd.download.JannovarDownloadOptions
 
setFromArgs(Namespace) - Method in class de.charite.compbio.jannovar.cmd.hgvs_to_vcf.ProjectTranscriptToChromosomeOptions
 
setFromArgs(Namespace) - Method in class de.charite.compbio.jannovar.cmd.JannovarAnnotationOptions
 
setFromArgs(Namespace) - Method in class de.charite.compbio.jannovar.cmd.JannovarBaseOptions
Get values from Namespace object
setFromArgs(Namespace) - Method in class de.charite.compbio.jannovar.cmd.JannovarDBOptions
 
setFromArgs(Namespace) - Method in class de.charite.compbio.jannovar.cmd.statistics.JannovarGatherStatisticsOptions
 
setFtpProxy(URL) - Method in class de.charite.compbio.jannovar.cmd.JannovarBaseOptions
 
setGeneIdentifiers(List<String>) - Method in class de.charite.compbio.jannovar.cmd.download.JannovarDownloadOptions
 
setGenomicChanges(List<String>) - Method in class de.charite.compbio.jannovar.cmd.annotate_pos.JannovarAnnotatePosOptions
 
setHttpProxy(URL) - Method in class de.charite.compbio.jannovar.cmd.JannovarBaseOptions
 
setHttpsProxy(URL) - Method in class de.charite.compbio.jannovar.cmd.JannovarBaseOptions
 
setInheritanceAnnoUseFilters(boolean) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setInterval(String) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setNt3PrimeShifting(boolean) - Method in class de.charite.compbio.jannovar.cmd.JannovarAnnotationOptions
 
setOffTargetFilterEnabled(boolean) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setOffTargetFilterIntronicSpliceIsOffTarget(boolean) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setOffTargetFilterUtrIsOffTarget(boolean) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setOneParentGtFilteredFiltersAffected(boolean) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setOutputFile(String) - Method in class de.charite.compbio.jannovar.cmd.download.JannovarDownloadOptions
 
setPathClinVar(String) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setPathCosmic(String) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setPathDbNsfp(String) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setPathFASTARef(String) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setPathInputText(String) - Method in class de.charite.compbio.jannovar.cmd.hgvs_to_vcf.ProjectTranscriptToChromosomeOptions
 
setPathInputVCF(String) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setPathInputVCF(String) - Method in class de.charite.compbio.jannovar.cmd.statistics.JannovarGatherStatisticsOptions
 
setPathOutputReport(String) - Method in class de.charite.compbio.jannovar.cmd.statistics.JannovarGatherStatisticsOptions
 
setPathOutputVCF(String) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setPathOutputVCF(String) - Method in class de.charite.compbio.jannovar.cmd.hgvs_to_vcf.ProjectTranscriptToChromosomeOptions
 
setPathPedFile(String) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setPathReferenceFASTA(String) - Method in class de.charite.compbio.jannovar.cmd.hgvs_to_vcf.ProjectTranscriptToChromosomeOptions
 
setPathThousandGenomes(String) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setPathVCFDBSNP(String) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setPathVCFExac(String) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setPathVCFGnomadExomes(String) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setPathVCFGnomadGenomes(String) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setPathVCFUK10K(String) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setPrefixClinVar(String) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setPrefixCosmic(String) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setPrefixDbNsfp(String) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setPrefixDBSNP(String) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setPrefixExac(String) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setPrefixGnomadExomes(String) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setPrefixGnomadGenomes(String) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setPrefixThousandGenomes(String) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setPrefixUK10K(String) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setReportProgress(boolean) - Method in class de.charite.compbio.jannovar.cmd.JannovarBaseOptions
 
setShowAll(boolean) - Method in class de.charite.compbio.jannovar.cmd.JannovarAnnotationOptions
 
setThreshDeNovoParentAd2(Integer) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setThreshFiltMaxAlleleFrequencyAd(double) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setThreshFiltMaxAlleleFrequencyAD(double) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setThreshFiltMaxAlleleFrequencyAr(double) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setThreshFiltMaxAlleleFrequencyAR(double) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setThreshFiltMaxCov(int) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setThreshFiltMaxExacHomAlt(int) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setThreshFiltMaxGtAafHet(double) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setThreshFiltMaxGtAafHomRef(double) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setThreshFiltMaxThousandGenomesHomAlt(int) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setThreshFiltMinGtAafHet(double) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setThreshFiltMinGtAafHomAlt(double) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setThreshFiltMinGtCovHet(int) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setThreshFiltMinGtCovHomAlt(int) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setThreshFiltMinGtGq(int) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setTsvAnnotationOptions(List<GenericTSVAnnotationOptions>) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setupParser(Subparsers) - Static method in class de.charite.compbio.jannovar.cmd.annotate_csv.JannovarAnnotateCSVOptions
Setup ArgumentParser
setupParser(Subparsers) - Static method in class de.charite.compbio.jannovar.cmd.annotate_pos.JannovarAnnotatePosOptions
Setup ArgumentParser
setupParser(Subparsers) - Static method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
Setup ArgumentParser
setupParser(Subparsers) - Static method in class de.charite.compbio.jannovar.cmd.db_list.JannovarDBListOptions
Setup ArgumentParser
setupParser(Subparsers) - Static method in class de.charite.compbio.jannovar.cmd.download.JannovarDownloadOptions
Setup ArgumentParser
setupParser(Subparsers) - Static method in class de.charite.compbio.jannovar.cmd.hgvs_to_vcf.ProjectTranscriptToChromosomeOptions
Setup ArgumentParser
setupParser(ArgumentParser) - Static method in class de.charite.compbio.jannovar.cmd.JannovarAnnotationOptions
Setup ArgumentParser
setupParser(ArgumentParser) - Static method in class de.charite.compbio.jannovar.cmd.JannovarBaseOptions
Setup global ArgumentParser
setupParser(Subparsers) - Static method in class de.charite.compbio.jannovar.cmd.statistics.JannovarGatherStatisticsOptions
Setup ArgumentParser
setUseAdvancedPedigreeFilters(boolean) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setUseParentGtIsFiltered(boolean) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setUseThreeLetterAminoAcidCode(boolean) - Method in class de.charite.compbio.jannovar.cmd.JannovarAnnotationOptions
 
setUseThresholdFilters(boolean) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setVcfAnnotationOptions(List<GenericVCFAnnotationOptions>) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setVerbosity(int) - Method in class de.charite.compbio.jannovar.cmd.JannovarBaseOptions
 
SIFT_converted_rankscore - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
SIFT_pred - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
SIFT_score - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
SiPhy_29way_logOdds - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
SiPhy_29way_logOdds_rankscore - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
SiPhy_29way_pi - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 

T

toString() - Method in class de.charite.compbio.jannovar.cmd.annotate_csv.JannovarAnnotateCSVOptions
 
toString() - Method in class de.charite.compbio.jannovar.cmd.annotate_pos.JannovarAnnotatePosOptions
 
toString() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions.BedAnnotationOptions
 
toString() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
toString() - Method in class de.charite.compbio.jannovar.cmd.download.JannovarDownloadOptions
 
toString() - Method in class de.charite.compbio.jannovar.cmd.hgvs_to_vcf.ProjectTranscriptToChromosomeOptions
 
toString() - Method in class de.charite.compbio.jannovar.cmd.JannovarAnnotationOptions
 
toString() - Method in class de.charite.compbio.jannovar.cmd.JannovarBaseOptions
 
toString() - Method in class de.charite.compbio.jannovar.cmd.JannovarDBOptions
 
toString() - Method in class de.charite.compbio.jannovar.cmd.statistics.JannovarGatherStatisticsOptions
 
Transcript_id_VEST3 - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
Transcript_var_VEST3 - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
TWINSUK_AC - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
TWINSUK_AF - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 

U

Uniprot_aapos_Polyphen2 - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
Uniprot_acc_Polyphen2 - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
Uniprot_id_Polyphen2 - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
useAdvancedPedigreeFilters - Variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
Whether or not to use the advanced pedigree filters (mainly useful for de novo variants)
useThresholdFilters - Variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
Whether or not to use threshold-based filters

V

VEST3_rankscore - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
VEST3_score - Static variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.DbNsfpFields
 
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