skills/onekgpd/references/annotation_vocabularies.md
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_ABLATIONSPLICE_ACCEPTOR_VARIANTSPLICE_DONOR_VARIANTSTOP_GAINEDFRAMESHIFT_VARIANTSTOP_LOSTSTART_LOSTTRANSCRIPT_AMPLIFICATIONINFRAME_INSERTIONINFRAME_DELETIONMISSENSE_VARIANTPROTEIN_ALTERING_VARIANTSPLICE_REGION_VARIANTINCOMPLETE_TERMINAL_CODON_VARIANTSTART_RETAINED_VARIANTSTOP_RETAINED_VARIANTSYNONYMOUS_VARIANTCODING_SEQUENCE_VARIANTMATURE_MIRNA_VARIANTFIVE_PRIME_UTR_VARIANTTHREE_PRIME_UTR_VARIANTNON_CODING_TRANSCRIPT_EXON_VARIANTINTRON_VARIANTNMD_TRANSCRIPT_VARIANTNON_CODING_TRANSCRIPT_VARIANTUPSTREAM_GENE_VARIANTDOWNSTREAM_GENE_VARIANTTFBS_ABLATIONTFBS_AMPLIFICATIONTF_BINDING_SITE_VARIANTREGULATORY_REGION_ABLATIONREGULATORY_REGION_AMPLIFICATIONFEATURE_ELONGATIONREGULATORY_REGION_VARIANTFEATURE_TRUNCATIONINTERGENIC_VARIANTSPLICE_POLYPYRIMIDINE_TRACT_VARIANTSPLICE_DONOR_5TH_BASE_VARIANTSPLICE_DONOR_REGION_VARIANTCODING_TRANSCRIPT_VARIANTSEQUENCE_VARIANT--impact4 terms:
HIGHMODERATELOWMODIFIER--variant-type34 terms:
SNVINSERTIONDELETIONINDELSUBSTITUTIONINVERSIONTRANSLOCATIONDUPLICATIONALU_INSERTIONCOMPLEX_STRUCTURAL_ALTERATIONCOMPLEX_SUBSTITUTIONCOPY_NUMBER_GAINCOPY_NUMBER_LOSSCOPY_NUMBER_VARIATIONINTERCHROMOSOMAL_BREAKPOINTINTERCHROMOSOMAL_TRANSLOCATIONINTRACHROMOSOMAL_BREAKPOINTINTRACHROMOSOMAL_TRANSLOCATIONLOSS_OF_HETEROZYGOSITYMOBILE_ELEMENT_DELETIONMOBILE_ELEMENT_INSERTIONNOVEL_SEQUENCE_INSERTIONSHORT_TANDEM_REPEAT_VARIATIONTANDEM_DUPLICATIONPROBEALU_DELETIONHERV_DELETIONHERV_INSERTIONLINE1_DELETIONLINE1_INSERTIONSVA_DELETIONSVA_INSERTIONCOMPLEX_CHROMOSOMAL_REARRANGEMENTSEQUENCE_ALTERATION--feature-type3 terms:
TRANSCRIPTREGULATORYFEATUREMOTIFFEATURE--bio-type47 terms:
PROCESSED_TRANSCRIPTLNCRNAANTISENSEMACRO_LNCRNANON_CODINGRETAINED_INTRONSENSE_INTRONICSENSE_OVERLAPPINGLINCRNANCRNAMIRNAMISCRNAPIRNARRNASIRNASNRNASNORNATRNAVAULTRNAPROTEIN_CODINGPSEUDOGENEIG_PSEUDOGENEPOLYMORPHIC_PSEUDOGENEPROCESSED_PSEUDOGENETRANSCRIBED_PSEUDOGENETRANSLATED_PSEUDOGENEUNITARY_PSEUDOGENEUNPROCESSED_PSEUDOGENEREADTHROUGHSTOP_CODON_READTHROUGHTECTR_GENETR_C_GENETR_D_GENETR_J_GENETR_V_GENEIG_GENEIG_C_GENEIG_D_GENEIG_J_GENEIG_V_GENENONSENSE_MEDIATED_DECAYPROMOTERPROMOTER_FLANKING_REGIONENHANCERCTCF_BINDING_SITEOPEN_CHROMATIN_REGION--clin-significance19 terms:
CLNSIG_BENIGNLIKELY_BENIGNUNCERTAIN_SIGNIFICANCELIKELY_PATHOGENICPATHOGENICDRUG_RESPONSEASSOCIATIONRISK_FACTORPROTECTIVEAFFECTSCONFERS_SENSITIVITYCONFLICTING_INTERPRETATIONSNOT_PROVIDEDOTHERLIKELY_PATHOGENIC_LOW_PENETRANCEPATHOGENIC_LOW_PENETRANCEUNCERTAIN_RISK_ALLELELIKELY_RISK_ALLELEESTABLISHED_RISK_ALLELE--alpha-missense-class3 terms:
AM_LIKELY_BENIGNAM_LIKELY_PATHOGENICAM_AMBIGUOUSCLNSIG_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.