Please update schema version

The JSON output from 3.11.1 is inconsistent with the latest documentation of the schema. I've also annotated the same file with 2.0.9, which is consistent with the documentation to show the key differences...at least the ones I was looking at:

dbsnp

Looks like these were moved back to the previous format of array strings. (consistent with version 5) 3.11.1 "dbsnp": ["rs370723703"],

2.0.9 "dbsnp": { "ids": ["rs370723703"] }

transcripts

Seems that these were changed to raw array of transcript objects instead of an object wrapper.

3.11.1

"transcripts": [{
        "transcript": "ENST00000442987.3",
        "source": "Ensembl",
        "bioType": "polymorphic_pseudogene",
        "geneId": "ENSG00000233750",
        "hgnc": "CICP27",
        "consequence": ["downstream_gene_variant"],
        "isCanonical": true
    }, {
        "transcript": "NR_039983.2",
        "source": "RefSeq",
        "bioType": "rRNA_pseudogene",
        "cdnaPos": "1034",
        "exons": "3/3",
        "geneId": "729737",
        "hgnc": "LOC729737",
        "consequence": ["non_coding_transcript_exon_variant"],
        "hgvsc": "NR_039983.2:n.1034T>C",
        "isCanonical": true
    }
]

2.0.9

"transcripts": {
    "refSeq": [{
            "transcript": "NR_039983.2",
            "bioType": "misc_RNA",
            "cdnaPos": "1034",
            "exons": "3/3",
            "geneId": "729737",
            "hgnc": "LOC729737",
            "consequence": ["non_coding_transcript_exon_variant"],
            "hgvsc": "NR_039983.2:n.1034T>C",
            "isCanonical": true
        }, {
            "transcript": "XR_246629.1",
            "bioType": "misc_RNA",
            "geneId": "100996442",
            "hgnc": "LOC100996442",
            "consequence": ["downstream_gene_variant"]
        }
    ],
    "ensembl": [{
            "transcript": "ENST00000442987.3",
            "bioType": "processed_pseudogene",
            "geneId": "ENSG00000233750",
            "hgnc": "CICP27",
            "consequence": ["downstream_gene_variant"],
            "isCanonical": true
        }
    ]
}

ClinVar

"significance" field has changed from single string to string list.

3.11.1

"clinvar": [{
        "id": "RCV000954365.1",
        "variationId": 281760,
        "reviewStatus": "criteria provided, single submitter",
        "alleleOrigins": ["germline"],
        "refAllele": "G",
        "altAllele": "A",
        "phenotypes": ["not provided"],
        "medGenIds": ["CN517202"],
        "significance": ["benign"],
        "lastUpdatedDate": "2019-12-17",
        "pubMedIds": ["28492532"],
        "isAlleleSpecific": true
    }, {
        "id": "RCV000337497.1",
        "variationId": 281760,
        "reviewStatus": "criteria provided, single submitter",
        "alleleOrigins": ["germline"],
        "refAllele": "G",
        "altAllele": "A",
        "phenotypes": ["not specified"],
        "medGenIds": ["CN169374"],
        "significance": ["benign"],
        "lastUpdatedDate": "2019-12-17",
        "isAlleleSpecific": true
    }
]

2.0.9

"clinvar": [{
        "id": "RCV000337497.1",
        "reviewStatus": "criteria provided, single submitter",
        "alleleOrigins": ["germline"],
        "refAllele": "G",
        "altAllele": "A",
        "phenotypes": ["not specified"],
        "medGenIds": ["CN169374"],
        "significance": "benign",
        "lastUpdatedDate": "2020-03-04",
        "isAlleleSpecific": true
    }, {
        "id": "RCV000954365.1",
        "reviewStatus": "criteria provided, single submitter",
        "alleleOrigins": ["germline"],
        "refAllele": "G",
        "altAllele": "A",
        "phenotypes": ["not provided"],
        "medGenIds": ["CN517202"],
        "significance": "benign",
        "lastUpdatedDate": "2020-03-04",
        "pubMedIds": ["28492532"],
        "isAlleleSpecific": true
    }
]

Illumina / Nirvana