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