Peter-J-Freeman
commented
3 years ago I have checked the APIs based on this afternoons chat and both tools have a light-weight batch mode.
The APIs are here http://rest.variantvalidator.org/
VariantValidator
NM_000088.3:c.589G>T|NM_000088.3:c.589-1G>T
{
"NM_000088.3:c.589-1G>T": {
"alt_genomic_loci": [],
"annotations": {
"chromosome": "17",
"db_xref": {
"CCDS": "CCDS11561.1",
"GeneID": "1277",
"HGNC": "2197",
"MIM": "120150",
"select": "RefSeq"
},
"gene_synonym": [
"EDSARTH1",
"EDSC",
"OI1",
"OI2",
"OI3",
"OI4"
],
"map": "17q21.33",
"note": "collagen type I alpha 1 chain",
"variant": "0"
},
"gene_ids": {
"ccds_ids": [
"CCDS11561"
],
"ensembl_gene_id": "ENSG00000108821",
"entrez_gene_id": "1277",
"hgnc_id": "HGNC:2197",
"omim_id": [
"120150"
],
"ucsc_id": "uc002iqm.4"
},
"gene_symbol": "COL1A1",
"genome_context_intronic_sequence": "NC_000017.11(NM_000088.3):c.589-1G>T",
"hgvs_lrg_transcript_variant": "LRG_1t1:c.589-1G>T",
"hgvs_lrg_variant": "LRG_1:g.8637G>T",
"hgvs_predicted_protein_consequence": {
"lrg_slr": "LRG_1p1:p.?",
"lrg_tlr": "LRG_1p1:p.?",
"slr": "NP_000079.2:p.?",
"tlr": "NP_000079.2:p.?"
},
"hgvs_refseqgene_variant": "NG_007400.1:g.8637G>T",
"hgvs_transcript_variant": "NM_000088.3:c.589-1G>T",
"primary_assembly_loci": {
"grch37": {
"hgvs_genomic_description": "NC_000017.10:g.48275364C>A",
"vcf": {
"alt": "A",
"chr": "17",
"pos": "48275364",
"ref": "C"
}
},
"grch38": {
"hgvs_genomic_description": "NC_000017.11:g.50198003C>A",
"vcf": {
"alt": "A",
"chr": "17",
"pos": "50198003",
"ref": "C"
}
},
"hg19": {
"hgvs_genomic_description": "NC_000017.10:g.48275364C>A",
"vcf": {
"alt": "A",
"chr": "chr17",
"pos": "48275364",
"ref": "C"
}
},
"hg38": {
"hgvs_genomic_description": "NC_000017.11:g.50198003C>A",
"vcf": {
"alt": "A",
"chr": "chr17",
"pos": "50198003",
"ref": "C"
}
}
},
"reference_sequence_records": {
"lrg": "http://ftp.ebi.ac.uk/pub/databases/lrgex/LRG_1.xml",
"protein": "https://www.ncbi.nlm.nih.gov/nuccore/NP_000079.2",
"refseqgene": "https://www.ncbi.nlm.nih.gov/nuccore/NG_007400.1",
"transcript": "https://www.ncbi.nlm.nih.gov/nuccore/NM_000088.3"
},
"refseqgene_context_intronic_sequence": "NG_007400.1(NM_000088.3):c.589-1G>T",
"selected_assembly": "GRCh38",
"submitted_variant": "NM_000088.3:c.589-1G>T",
"transcript_description": "Homo sapiens collagen type I alpha 1 chain (COL1A1), mRNA",
"validation_warnings": []
},
"NM_000088.3:c.589G>T": {
"alt_genomic_loci": [],
"annotations": {
"chromosome": "17",
"db_xref": {
"CCDS": "CCDS11561.1",
"GeneID": "1277",
"HGNC": "2197",
"MIM": "120150",
"select": "RefSeq"
},
"gene_synonym": [
"EDSARTH1",
"EDSC",
"OI1",
"OI2",
"OI3",
"OI4"
],
"map": "17q21.33",
"note": "collagen type I alpha 1 chain",
"variant": "0"
},
"gene_ids": {
"ccds_ids": [
"CCDS11561"
],
"ensembl_gene_id": "ENSG00000108821",
"entrez_gene_id": "1277",
"hgnc_id": "HGNC:2197",
"omim_id": [
"120150"
],
"ucsc_id": "uc002iqm.4"
},
"gene_symbol": "COL1A1",
"genome_context_intronic_sequence": "",
"hgvs_lrg_transcript_variant": "LRG_1t1:c.589G>T",
"hgvs_lrg_variant": "LRG_1:g.8638G>T",
"hgvs_predicted_protein_consequence": {
"lrg_slr": "LRG_1p1:p.(G197C)",
"lrg_tlr": "LRG_1p1:p.(Gly197Cys)",
"slr": "NP_000079.2:p.(G197C)",
"tlr": "NP_000079.2:p.(Gly197Cys)"
},
"hgvs_refseqgene_variant": "NG_007400.1:g.8638G>T",
"hgvs_transcript_variant": "NM_000088.3:c.589G>T",
"primary_assembly_loci": {
"grch37": {
"hgvs_genomic_description": "NC_000017.10:g.48275363C>A",
"vcf": {
"alt": "A",
"chr": "17",
"pos": "48275363",
"ref": "C"
}
},
"grch38": {
"hgvs_genomic_description": "NC_000017.11:g.50198002C>A",
"vcf": {
"alt": "A",
"chr": "17",
"pos": "50198002",
"ref": "C"
}
},
"hg19": {
"hgvs_genomic_description": "NC_000017.10:g.48275363C>A",
"vcf": {
"alt": "A",
"chr": "chr17",
"pos": "48275363",
"ref": "C"
}
},
"hg38": {
"hgvs_genomic_description": "NC_000017.11:g.50198002C>A",
"vcf": {
"alt": "A",
"chr": "chr17",
"pos": "50198002",
"ref": "C"
}
}
},
"reference_sequence_records": {
"lrg": "http://ftp.ebi.ac.uk/pub/databases/lrgex/LRG_1.xml",
"protein": "https://www.ncbi.nlm.nih.gov/nuccore/NP_000079.2",
"refseqgene": "https://www.ncbi.nlm.nih.gov/nuccore/NG_007400.1",
"transcript": "https://www.ncbi.nlm.nih.gov/nuccore/NM_000088.3"
},
"refseqgene_context_intronic_sequence": "",
"selected_assembly": "GRCh38",
"submitted_variant": "NM_000088.3:c.589G>T",
"transcript_description": "Homo sapiens collagen type I alpha 1 chain (COL1A1), mRNA",
"validation_warnings": []
},
"flag": "gene_variant",
"metadata": {
"seqrepo_db": "2018-08-21",
"uta_schema": "uta_20180821",
"variantvalidator_hgvs_version": "1.2.5.vv1",
"variantvalidator_version": "1.0.4.dev125+gd3e875e"
}
}LOVD
NC_000017.10:g.48275363C>A|NC_000017.11:g.50198003C>A
{
"NC_000017.10:g.48275363C>A": {
"NC_000017.10:g.48275363C>A": {
"g_hgvs": null,
"genomic_variant_error": "chromosome ID NC_000017.10 is not associated with genome build GRCh38",
"hgvs_t_and_p": null,
"p_vcf": null,
"selected_build": "GRCh38"
},
"errors": [],
"flag": "genomic_variant_warning"
},
"NC_000017.11:g.50198003C>A": {
"NC_000017.11:g.50198003C>A": {
"g_hgvs": "NC_000017.11:g.50198003C>A",
"genomic_variant_error": null,
"hgvs_t_and_p": {
"NM_000088.3": {
"alt_genomic_loci": {
"grch37": {},
"grch38": {},
"hg19": {},
"hg38": {}
},
"gap_statement": null,
"gapped_alignment_warning": null,
"p_hgvs_slc": "NP_000079.2:p.?",
"p_hgvs_tlc": "NP_000079.2:p.?",
"primary_assembly_loci": {
"grch37": {
"NC_000017.11": {
"hgvs_genomic_description": "NC_000017.11:g.50198003C>A",
"vcf": {
"alt": "A",
"chr": "NC_000017.11",
"pos": "50198003",
"ref": "C"
}
}
},
"grch38": {
"NC_000017.11": {
"hgvs_genomic_description": "NC_000017.11:g.50198003C>A",
"vcf": {
"alt": "A",
"chr": "NC_000017.11",
"pos": "50198003",
"ref": "C"
}
}
},
"hg19": {
"NC_000017.11": {
"hgvs_genomic_description": "NC_000017.11:g.50198003C>A",
"vcf": {
"alt": "A",
"chr": "NC_000017.11",
"pos": "50198003",
"ref": "C"
}
}
},
"hg38": {
"NC_000017.11": {
"hgvs_genomic_description": "NC_000017.11:g.50198003C>A",
"vcf": {
"alt": "A",
"chr": "NC_000017.11",
"pos": "50198003",
"ref": "C"
}
}
}
},
"t_hgvs": "NM_000088.3:c.589-1G>T",
"transcript_variant_error": null
}
},
"p_vcf": "17:50198003:C:A",
"selected_build": "GRCh38"
},
"errors": [],
"flag": null
},
"metadata": {
"seqrepo_db": "/local/seqrepo/2018-08-21",
"uta_schema": "uta_20180821",
"variantformatter_version": "1.0.2.dev26+gcbd8fb1",
"variantvalidator_hgvs_version": "1.2.5.vv1",
"variantvalidator_version": "1.0.4.dev125+gd3e875e"
}
}When we build, I think that Validator should be used as the transcript validation tool and LOVD as the genomic variant validation tool. We can add gene information to the output very easily if needed.
The only slight issues is that, as @ifokkema once pointed out, that the | is now used by HGVS. I need to have a chat with Johan about reserving at least 1 symbol for delimiting. Perhaps the backslash?
ifokkema
leicray
John-F-Wagstaff
Opening an issue to plan the integration.
Inviting comment from @leicray @John-F-Wagstaff @ifokkema.
Note. I will be starting this process next week (22nd/23rd March) and will use this issue to log progress and take feedback from you all.
Cheers