This is a work in progress documentation for v2.0.0 |
Genomic variant data model plays a crucial role not only in OpenCGA but also in OpenCB suite. Variant data model provides a generic way of representing any variant with any other interesting information associated with it. Variant data model is heavily used in OpenCGA when loading VCF files or when exporting query results. Variant data model is implemented in OpenCB Biodata project, this allows the rest of OpenCB projects such as CellBase to use it.
Main goals of variant data model include:
Some of the main features of the variant data model include:
A high level representation of the variant looks like this, only main categories are shown:
{ "id": "1:69511:A:G", "names": ["rs75062661"], "chromosome": "1", "start": 69511, "end": 69511, "strand": "+", "length": 1, "type": "SNV", "reference": "A", "alternate": "G", "studies": [ { "studyId": "demo@family:corpasome", "secondaryAlternates": [], "files": [ { "fileId": "quartet.variants.annotated.vcf.gz" "call" : {}, "data": { "FILTER": "PASS", "QUAL": "4293.01", "HaplotypeScore": "2.4399", "MQ": "15.47", ... } }, ... ], "sampleDataKeys": ["GT", "AD", "DP", "GQ", "PL"], "samples": [ { "sampleId": "ISBM200170115", "fileIndex": 0, "data": ["1/1", "2,171", "173", "99", "2218,228,0"] }, ... ], "stats": [ { "cohortId": "ALL", "sampleCount": 4, "fileCount": 1, "alleleCount": 8, "refAlleleCount": 0, "refAlleleFreq": 0.0, "altAlleleCount": 8, "altAlleleFreq": 1.0, "genotypeCount": { "0/0": 0, "0/1": 0, "1/1": 4 }, "genotypeFreq": { "0/0": 0.0, "0/1": 0.0, "1/1": 1.0 }, "missingAlleleCount": 0, "missingGenotypeCount": 0, "maf": 0.0, "mafAllele": "A", "mgf": 0.0, "mgfGenotype": "0/0", "filterCount": { "PASS": 0, "VQSRTrancheSNP99.90to100.00": 1 }, "filterFreq": { "PASS": 0.0, "VQSRTrancheSNP99.90to100.00": 1.0 }, "qualityCount": 1, "qualityAvg": 4293.01 }, ... ], "scores": [], "issues": [] } ], "annotation": { "id": "rs2691305", "chromosome": "1", "start": 69511, "reference": "A", "alternate": "G", "hgvs": ["ENST00000335137(ENSG00000186092):c.421A>G"], "displayConsequenceType": "missense_variant", "consequenceTypes": [ { "geneName": "OR4F5", "ensemblGeneId": "ENSG00000186092", "ensemblTranscriptId": "ENST00000335137", "biotype": "protein_coding", "cdnaPosition": 421, "cdsPosition": 421, "codon": "Aca/Gca", "strand": "+", "transcriptAnnotationFlags": ["CCDS", "basic"], "exonOverlap": [ { "number": "1/1", "percentage": 0.108932465 } ], "proteinVariantAnnotation": { "uniprotAccession": "Q8NH21", "position": 141, "reference": "THR", "alternate": "ALA", "features": [ { "id": "IPR017452", "start": 34, "end": 280, "description": "GPCR, rhodopsin-like, 7TM" }, ... ], "keywords": ["Cell membrane", "Complete proteome", "Disulfide bond", ...], "substitutionScores": [ { "description": "tolerated", "score": 0.63, "source": "sift" }, { "description": "benign", "score": 0.003, "source": "polyphen" } ], }, "sequenceOntologyTerms": [ { "accession": "SO:0001583", "name": "missense_variant" } ] } ], "conservation": [ { "score": 1.149999976158142, "source": "gerp" }, { "score": 0.1289999932050705, "source": "phastCons" }, { "score": -0.527999997138977, "source": "phylop" } ], "cytoband": [ { "name": "p36.33", "chromosome": "1", "start": 1, "end": 2300000, "stain": "gneg" } ], "functionalScore": [ { "score": -0.7899999618530273, "source": "cadd_raw" }, { "score": 0.03999999910593033, "source": "cadd_scaled" } ], "geneDrugInteraction": [], "geneTraitAssociation": [], "populationFrequencies": [ { "altAllele": "G", "altAlleleFreq": 0.84222084, "altHomGenotypeFreq": 0.77478045, "hetGenotypeFreq": 0.1348808, "population": "ALL", "refAllele": "A", "refAlleleFreq": 0.15777917, "refHomGenotypeFreq": 0.090338774, "study": "GNOMAD_GENOMES" }, { "altAllele": "G", "altAlleleFreq": 0.9637507, "altHomGenotypeFreq": 0.94847214, "hetGenotypeFreq": 0.03055722, "population": "NFE", "refAllele": "A", "refAlleleFreq": 0.03624925, "refHomGenotypeFreq": 0.02097064, "study": "GNOMAD_GENOMES" } ], "repeat": [ { "chromosome": "1", "copyNumber": 2.0, "end": 87112, "id": "9119", "percentageMatch": 0.992904, "source": "genomicSuperDup", "start": 10001 }, { "chromosome": "1", "copyNumber": 2.0, "end": 87112, "id": "14903", "percentageMatch": 0.995437, "source": "genomicSuperDup", "start": 18393 } ], "traitAssociation": [ { "additionalProperties": [ { "name": "mutationSomaticStatus_in_source_file", "value": "Confirmed " "somatic " "variant"}], "alleleOrigin": [], "bibliography": [], "ethnicity": "Z", "genomicFeatures": [{"featureType": "gene", "xrefs": {"symbol": "OR4F5"}}, {"featureType": "gene", "xrefs": {"symbol": "8301"}}], "heritableTraits": [], "id": "COSM4144171", "somaticInformation": {"histologySubtype": "neoplasm", "primaryHistology": "other", "primarySite": "thyroid", "sampleSource": "", "tumourOrigin": ""}, "source": {"name": "cosmic"}, "submissions": []}]} "additionalAttributes": { "opencga": { "attribute": { "annotationId": "CURRENT", "release": "1" } } } } |
Variant data model is implemented in OpenCB Biodata project, this allows the rest of OpenCB projects such as CellBase, Oskar to
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