Controlled-vocabulary terms accepted by the CSV annotation-filter flags of
onekgpd_api.py. Values are case-insensitive and resolved by exact member
name; pass them as comma-separated lists (e.g.
--consequence MISSENSE_VARIANT,STOP_GAINED). Multiple values within one flag
are combined with OR; different flags combine with AND.
These lists are the complete set of valid tokens for each flag. A value not in the relevant list is rejected with an error listing the valid values.
--consequence41 terms:
- TRANSCRIPT_ABLATION
- SPLICE_ACCEPTOR_VARIANT
- SPLICE_DONOR_VARIANT
- STOP_GAINED
- FRAMESHIFT_VARIANT
- STOP_LOST
- START_LOST
- TRANSCRIPT_AMPLIFICATION
- INFRAME_INSERTION
- INFRAME_DELETION
- MISSENSE_VARIANT
- PROTEIN_ALTERING_VARIANT
- SPLICE_REGION_VARIANT
- INCOMPLETE_TERMINAL_CODON_VARIANT
- START_RETAINED_VARIANT
- STOP_RETAINED_VARIANT
- SYNONYMOUS_VARIANT
- CODING_SEQUENCE_VARIANT
- MATURE_MIRNA_VARIANT
- FIVE_PRIME_UTR_VARIANT
- THREE_PRIME_UTR_VARIANT
- NON_CODING_TRANSCRIPT_EXON_VARIANT
- INTRON_VARIANT
- NMD_TRANSCRIPT_VARIANT
- NON_CODING_TRANSCRIPT_VARIANT
- UPSTREAM_GENE_VARIANT
- DOWNSTREAM_GENE_VARIANT
- TFBS_ABLATION
- TFBS_AMPLIFICATION
- TF_BINDING_SITE_VARIANT
- REGULATORY_REGION_ABLATION
- REGULATORY_REGION_AMPLIFICATION
- FEATURE_ELONGATION
- REGULATORY_REGION_VARIANT
- FEATURE_TRUNCATION
- INTERGENIC_VARIANT
- SPLICE_POLYPYRIMIDINE_TRACT_VARIANT
- SPLICE_DONOR_5TH_BASE_VARIANT
- SPLICE_DONOR_REGION_VARIANT
- CODING_TRANSCRIPT_VARIANT
- SEQUENCE_VARIANT
--impact4 terms:
- HIGH
- MODERATE
- LOW
- MODIFIER
--variant-type34 terms:
- SNV
- INSERTION
- DELETION
- INDEL
- SUBSTITUTION
- INVERSION
- TRANSLOCATION
- DUPLICATION
- ALU_INSERTION
- COMPLEX_STRUCTURAL_ALTERATION
- COMPLEX_SUBSTITUTION
- COPY_NUMBER_GAIN
- COPY_NUMBER_LOSS
- COPY_NUMBER_VARIATION
- INTERCHROMOSOMAL_BREAKPOINT
- INTERCHROMOSOMAL_TRANSLOCATION
- INTRACHROMOSOMAL_BREAKPOINT
- INTRACHROMOSOMAL_TRANSLOCATION
- LOSS_OF_HETEROZYGOSITY
- MOBILE_ELEMENT_DELETION
- MOBILE_ELEMENT_INSERTION
- NOVEL_SEQUENCE_INSERTION
- SHORT_TANDEM_REPEAT_VARIATION
- TANDEM_DUPLICATION
- PROBE
- ALU_DELETION
- HERV_DELETION
- HERV_INSERTION
- LINE1_DELETION
- LINE1_INSERTION
- SVA_DELETION
- SVA_INSERTION
- COMPLEX_CHROMOSOMAL_REARRANGEMENT
- SEQUENCE_ALTERATION
--feature-type3 terms:
- TRANSCRIPT
- REGULATORYFEATURE
- MOTIFFEATURE
--bio-type47 terms:
- PROCESSED_TRANSCRIPT
- LNCRNA
- ANTISENSE
- MACRO_LNCRNA
- NON_CODING
- RETAINED_INTRON
- SENSE_INTRONIC
- SENSE_OVERLAPPING
- LINCRNA
- NCRNA
- MIRNA
- MISCRNA
- PIRNA
- RRNA
- SIRNA
- SNRNA
- SNORNA
- TRNA
- VAULTRNA
- PROTEIN_CODING
- PSEUDOGENE
- IG_PSEUDOGENE
- POLYMORPHIC_PSEUDOGENE
- PROCESSED_PSEUDOGENE
- TRANSCRIBED_PSEUDOGENE
- TRANSLATED_PSEUDOGENE
- UNITARY_PSEUDOGENE
- UNPROCESSED_PSEUDOGENE
- READTHROUGH
- STOP_CODON_READTHROUGH
- TEC
- TR_GENE
- TR_C_GENE
- TR_D_GENE
- TR_J_GENE
- TR_V_GENE
- IG_GENE
- IG_C_GENE
- IG_D_GENE
- IG_J_GENE
- IG_V_GENE
- NONSENSE_MEDIATED_DECAY
- PROMOTER
- PROMOTER_FLANKING_REGION
- ENHANCER
- CTCF_BINDING_SITE
- OPEN_CHROMATIN_REGION
--clin-significance19 terms:
- CLNSIG_BENIGN
- LIKELY_BENIGN
- UNCERTAIN_SIGNIFICANCE
- LIKELY_PATHOGENIC
- PATHOGENIC
- DRUG_RESPONSE
- ASSOCIATION
- RISK_FACTOR
- PROTECTIVE
- AFFECTS
- CONFERS_SENSITIVITY
- CONFLICTING_INTERPRETATIONS
- NOT_PROVIDED
- OTHER
- LIKELY_PATHOGENIC_LOW_PENETRANCE
- PATHOGENIC_LOW_PENETRANCE
- UNCERTAIN_RISK_ALLELE
- LIKELY_RISK_ALLELE
- ESTABLISHED_RISK_ALLELE
--alpha-missense-class3 terms:
- AM_LIKELY_BENIGN
- AM_LIKELY_PATHOGENIC
- AM_AMBIGUOUS
CLNSIG_BENIGN (note the CLNSIG_ prefix);
all other ClinSignificance tokens are the bare term.--alpha-missense-score-lt/-gt): set one or the other, not both.