{
    "$schema": "https://raw.githubusercontent.com/BfArM-MVH/MVGenomseq/refs/tags/v1.3.0/GRZ/grz-schema.json",
    "submission": {
        "submissionDate": "2024-12-10",
        "submissionType": "test",
        "tanG": "a2b6c3d9e8f7123456789abcdef0123456789abcdef0123456789abcdef01234",
        "localCaseId": "CASE12345",
        "coverageType": "GKV",
        "submitterId": "260913195",
        "genomicDataCenterId": "GRZM00006",
        "clinicalDataNodeId": "KDKTUE005",
        "diseaseType": "rare",
        "genomicStudyType": "single",
        "genomicStudySubtype": "germline-only",
        "labName": "Genomics Lab Humangenetik MRI"
    },
    "donors": [
        {
            "donorPseudonym": "a2b6c3d9e8f7123456789abcdef0123456789abcdef0123456789abcdef01234",
            "gender": "other",
            "relation": "index",
            "mvConsent": {
                "presentationDate": "2023-06-10",
                "version": "1.0",
                "scope": [
                    {
                        "type": "permit",
                        "date": "2023-06-10",
                        "domain": "mvSequencing"
                    }
                ]
            },
            "researchConsents": [
                {
                    "schemaVersion": "2025.0.1",
                    "presentationDate": "2023-06-10",
                    "noScopeJustification": "consent information cannot be submitted by LE due to technical reason"
                }
            ],
            "labData": [
                {
                    "labDataName": "Blood DNA normal",
                    "tissueOntology": {
                        "name": "UBERON",
                        "version": "1.5"
                    },
                    "tissueTypeId": "UBERON:0000178",
                    "tissueTypeName": "blood",
                    "sampleDate": "2023-06-21",
                    "sampleConservation": "cryo-frozen",
                    "sequenceType": "dna",
                    "sequenceSubtype": "other",
                    "fragmentationMethod": "none",
                    "libraryType": "wgs_lr",
                    "libraryPrepKit": "SMRTbell prep kit 3.0",
                    "libraryPrepKitManufacturer": "PacBio",
                    "sequencerModel": "PacBio Sequel II",
                    "sequencerManufacturer": "PacBio",
                    "kitName": "SMRTbell™ Express Template Prep Kit",
                    "kitManufacturer": "PacBio",
                    "enrichmentKitManufacturer": "other",
                    "enrichmentKitDescription": "SMRTbell™ DNA Template Prep Kit",
                    "barcode": "NA12345",
                    "sequencingLayout": "single-end",
                    "tumorCellCount": [
                        {
                            "count": 80,
                            "method": "bioinformatics"
                        }
                    ],
                    "sequenceData": {
                        "bioinformaticsPipelineName": "DNASeq_Pipeline_XYZ",
                        "bioinformaticsPipelineVersion": "v3.4.1",
                        "referenceGenome": "GRCh38",
                        "percentBasesAboveQualityThreshold": {
                                "minimumQuality": 50,
                                "percent": 88
                        },
                        "meanDepthOfCoverage": 40,
                        "minCoverage": 30,

                        "targetedRegionsAboveMinCoverage": 0.9,
                        "nonCodingVariants": true,
                        "callerUsed": [
                            {
                                "name": "deepvariant",
                                "version": "0.2.3"
                            }
                        ],
                        "files": [
                            {
                                "filePath": "donor_001/m84011_220902_175841_s1.hifi_reads.bam",
                                "fileType": "bam",
                                "checksumType": "sha256",
                                "fileChecksum": "9b1abb613b382bf274ee8da3cc8bd77d8e8cbebf9f1571f2b02a09f3967f2d60",
                                "fileSizeInBytes": 45756630027,
                                "readLength": 15474
                            },
                            {
                                "filePath": "donor_001/HG002.m84011_220902_175841_s1.GRCh38.deepvariant.phased.vcf.gz",
                                "fileType": "vcf",
                                "checksumType": "sha256",
                                "fileChecksum": "73cd6230ca2f8f4d51a0f4023bd99c2291cf01ea2499575f98704182a07fde87",
                                "fileSizeInBytes": 150635503                                              
                            } 
                        ]
                    }
                }
            ]
        }
    ]
}
