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scripts/variantstore/wdl/schemas/variant_transcript_schema.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,224 @@ | ||
| [ | ||
| { | ||
| "description": "Must be positive. Exact position for a SNP and the position before the alteration in an indel", | ||
| "name": "position", | ||
| "type": "Integer", | ||
| "mode": "Required" | ||
| }, | ||
| { | ||
| "description": "Variant ID. Unique string for identifying a variant (as produced by NIRVANA based on a spec from Broad Institute)", | ||
| "name": "vid", | ||
| "type": "String", | ||
| "mode": "Required" | ||
| }, | ||
| { | ||
| "description": "Contig names match the hg38 reference", | ||
| "name": "contig", | ||
| "type": "String", | ||
| "mode": "Required" | ||
| }, | ||
| { | ||
| "description": "base(s). This should always be one base for SNPs and insertions. More than one base for deletions", | ||
| "name": "ref_allele", | ||
| "type": "String", | ||
| "mode": "Required" | ||
| }, | ||
| { | ||
| "description": "base(s). This should always be one base for SNPs and deletions. More than one base for insertions", | ||
| "name": "alt_allele", | ||
| "type": "String", | ||
| "mode": "Required" | ||
| }, | ||
| { | ||
| "description": "DNA change type (HGVS)", | ||
| "name": "variant_type", | ||
| "type": "String", | ||
| "mode": "Required" | ||
| }, | ||
| { | ||
| "description": "HGVS g. nomenclature Variant location", | ||
| "name": "genomic_location", | ||
| "type": "String", | ||
| "mode": "Required" | ||
| }, | ||
| { | ||
| "description": "rsID", | ||
| "name": "dbsnp_rsid", | ||
| "type": "String", | ||
| "mode": "Repeated" | ||
| }, | ||
| { | ||
| "description": "Transcript ID. Null indicates that this variant does not overlap any transcripts", | ||
| "name": "transcript", | ||
| "type": "String", | ||
| "mode": "Nullable" | ||
| }, | ||
| { | ||
| "description": "Gene symbol. A variant can have more than one associated gene symbol, since about 3% of genes do overlap", | ||
| "name": "gene_symbol", | ||
| "type": "String", | ||
| "mode": "Nullable" | ||
| }, | ||
| { | ||
| "description": "", | ||
| "name": "transcript_source", | ||
| "type": "String", | ||
| "mode": "Nullable" | ||
| }, | ||
| { | ||
| "description": "HGVS p. nomenclature; Amino acid change", | ||
| "name": "aa_change", | ||
| "type": "String", | ||
| "mode": "Nullable" | ||
| }, | ||
| { | ||
| "description": "Amino acid change type TODO check with Lee about why this json thinks its Repeated not nullable", | ||
| "name": "consequence", | ||
| "type": "String", | ||
| "mode": "Repeated" | ||
| }, | ||
| { | ||
| "description": "HGVS c. nomenclature; DNA change in transcript space", | ||
| "name": "dna_change_in_transcript", | ||
| "type": "String", | ||
| "mode": "Nullable" | ||
| }, | ||
| { | ||
| "description": "Exon number", | ||
| "name": "exon_number", | ||
| "type": "String", | ||
| "mode": "Nullable" | ||
| }, | ||
| { | ||
| "description": "Intron number", | ||
| "name": "intron_number", | ||
| "type": "String", | ||
| "mode": "Nullable" | ||
| }, | ||
| { | ||
| "description": "Gene ID for the transcript", | ||
| "name": "gene_id", | ||
| "type": "String", | ||
| "mode": "Nullable" | ||
| }, | ||
| { | ||
| "description": "Primary Transcript ID", | ||
| "name": "is_canonical_transcript", | ||
| "type": "Boolean", | ||
| "mode": "Nullable" | ||
| }, | ||
| { | ||
| "description": "AC TODO -- this needs to be added back and swapped to required -- Lee said this was a string?", | ||
| "name": "gvs_all_ac", | ||
| "type": "Integer", | ||
| "mode": "Nullable" | ||
| }, | ||
| { | ||
| "description": "AN TODO -- this needs to be added back and swapped to required", | ||
| "name": "gvs_all_an", | ||
| "type": "Integer", | ||
| "mode": "Nullable" | ||
| }, | ||
| { | ||
| "description": "AF TODO -- this needs to be added back and swapped to required -- Lee said this was a Float?", | ||
| "name": "gvs_all_af", | ||
| "type": "INTEGER", | ||
| "mode": "Nullable" | ||
| }, | ||
| { | ||
| "description": "REVEL", | ||
| "name": "revel", | ||
| "type": "FLOAT", | ||
| "mode": "Nullable" | ||
| }, | ||
| { | ||
| "description": "Slice AI", | ||
| "name": "splice_ai_acceptor_gain_score", | ||
| "type": "Float", | ||
| "mode": "Nullable" | ||
| }, | ||
| { | ||
| "description": "Slice AI", | ||
| "name": "splice_ai_acceptor_gain_distance", | ||
| "type": "Integer", | ||
| "mode": "Nullable" | ||
| }, | ||
| { | ||
| "description": "Slice AI", | ||
| "name": "splice_ai_acceptor_loss_score", | ||
| "type": "Float", | ||
| "mode": "Nullable" | ||
| }, | ||
| { | ||
| "description": "Slice AI", | ||
| "name": "splice_ai_acceptor_loss_distance", | ||
| "type": "Integer", | ||
| "mode": "Nullable" | ||
| }, | ||
| { | ||
| "description": "Slice AI", | ||
| "name": "splice_ai_donor_gain_score", | ||
| "type": "Float", | ||
| "mode": "Nullable" | ||
| }, | ||
| { | ||
| "description": "Slice AI", | ||
| "name": "splice_ai_donor_gain_distance", | ||
| "type": "Integer", | ||
| "mode": "Nullable" | ||
| }, | ||
| { | ||
| "description": "Slice AI", | ||
| "name": "splice_ai_donor_loss_score", | ||
| "type": "Float", | ||
| "mode": "Nullable" | ||
| }, | ||
| { | ||
| "description": "Slice AI", | ||
| "name": "splice_ai_donor_loss_distance", | ||
| "type": "Integer", | ||
| "mode": "Nullable" | ||
| }, | ||
| { | ||
| "description": "ClinVar Id for Validation", | ||
| "name": "clinvar_id", | ||
| "type": "String", | ||
| "mode": "Repeated" | ||
| }, | ||
| { | ||
| "description": "ClinVar Classification", | ||
| "name": "clinvar_classification", | ||
| "type": "String", | ||
| "mode": "Repeated" | ||
| }, | ||
| { | ||
| "description": "ClinVar Classification Date", | ||
| "name": "clinvar_last_updated", | ||
| "type": "Date", | ||
| "mode": "Nullable" | ||
| }, | ||
| { | ||
| "description": "ClinVar Disease Name", | ||
| "name": "clinvar_phenotype", | ||
| "type": "String", | ||
| "mode": "Repeated" | ||
| }, | ||
| { | ||
| "description": "gnomAD: 'Total' frequency", | ||
| "name": "gnomad_all_af", | ||
| "type": "Float", | ||
| "mode": "Nullable" | ||
| }, | ||
| { | ||
| "description": "gnomAD: 'Total' allele count", | ||
| "name": "gnomad_all_ac", | ||
| "type": "Integer", | ||
| "mode": "Nullable" | ||
| }, | ||
| { | ||
| "description": "gnomAD: 'Total' allele number", | ||
| "name": "gnomad_all_an", | ||
| "type": "Integer", | ||
| "mode": "Nullable" | ||
| } | ||
| ] |