- Created by Nacho Medina on Mar 23, 2020
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Overview
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 resto of OpenCB projects such as CellBase to use it.
Goals
Main goals of variant data model include:
- To be able represent any type of variant (SNV, INDEL) or structural variant (INSERTION, DELETION, CNV, TRANSLOCATION, ...), this includes phased variants and non-diploid organisms.
- To provide a file-format agnostic solution of storing genomic variant data from VCF, gVCF, microarrays, ...
- To allow bioinformaticians to add valuable and rich annotations fo researchers and clinicians
Main Features
Some of the main features of the variant data model include:
Design
A high level representation of the variant looks like this:
{ "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", "files": [ { "fileId": "quartet.variants.annotated.vcf.gz" "call" : { }, "data": { "ABHom": "0.982", "AC": "8", "AF": "1.00", "AN": "8", "BaseQRankSum": "2.089", "DB": "true", "DP": "331", "Dels": "0.00", "EFF": "NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T141A|305|OR4F5||CODING|NM_001005484.1|1|1)", "FILTER": "VQSRTrancheSNP99.90to100.00", "FS": "8.817", "HaplotypeScore": "2.4399", "MLEAC": "8", "MLEAF": "1.00", "MQ": "15.47", "MQ0": "145", "MQRankSum": "-0.047", "OND": "0.018", "QD": "12.97", "QUAL": "4293.01", "ReadPosRankSum": "1.662", "SB": "-1.450e+03", "VCF_ID": "rs75062661", "VQSLOD": "-14.4975", "culprit": "MQ", "set": "FilteredInAll" } } ], "secondaryAlternates": [], "sampleDataKeys": ["GT", "AD", "DP", "GQ", "PL"], "samples": [ { "sampleId": "", "fileIndex": 1, "data": ["1/1", "2,171", "173", "99", "2218,228,0"] }, { "sampleId": "", "fileIndex": 1, "data": ["1/1", "0,33", "34", "60", "508,60,0"] }, { "sampleId": "", "fileIndex": 1, "data": ["1/1", "0,61", "63", "93", "777,93,0"] }, { "sampleId": "", "fileIndex": 1, "data": ["1/1", "0,61", "61", "96", "790,96,0"]} ], "issues": [], "scores": [], "stats": {"ALL": {"alleleCount": 8, "altAlleleCount": 8, "altAlleleFreq": 1.0, "filterCount": {"PASS": 0, "VQSRTrancheSNP99.90to100.00": 1}, "filterFreq": {"PASS": 0.0, "VQSRTrancheSNP99.90to100.00": 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}, "maf": 0.0, "mafAllele": "A", "mgf": 0.0, "mgfGenotype": "0/0", "missingAlleleCount": 0, "missingGenotypeCount": 0, "qualityAvg": 4293.01, "refAlleleCount": 0, "refAlleleFreq": 0.0} }, }], "annotation": { "additionalAttributes": { "opencga": { "attribute": { "annotationId": "CURRENT", "release": "1" } } }, "alternate": "G", "chromosome": "1", "consequenceTypes": [ { "biotype": "protein_coding", "cdnaPosition": 421, "cdsPosition": 421, "codon": "Aca/Gca", "ensemblGeneId": "ENSG00000186092", "ensemblTranscriptId": "ENST00000335137", "exonOverlap": [{"number": "1/1", "percentage": 0.108932465}], "geneName": "OR4F5", "proteinVariantAnnotation": {"alternate": "ALA", "features": [{"description": "GPCR, " "rhodopsin-like, " "7TM", "end": 280, "id": "IPR017452", "start": 34}, {"end": 182, "start": 90, "type": "disulfide " "bond"}, {"description": "Helical; " "Name=4", "end": 151, "start": 133, "type": "transmembrane " "region"}, {"description": "Olfactory " "receptor " "4F5", "end": 305, "id": "PRO_0000150547", "start": 1, "type": "chain"}], "keywords": ["Cell " "membrane", "Complete " "proteome", "Disulfide " "bond", "G-protein " "coupled " "receptor", "Membrane", "Olfaction", "Receptor", "Reference " "proteome", "Sensory " "transduction", "Transducer", "Transmembrane", "Transmembrane " "helix"], "position": 141, "reference": "THR", "substitutionScores": [{"description": "tolerated", "score": 0.63, "source": "sift"}, {"description": "benign", "score": 0.003, "source": "polyphen"}], "uniprotAccession": "Q8NH21"}, "sequenceOntologyTerms": [{"accession": "SO:0001583", "name": "missense_variant"}], "strand": "+", "transcriptAnnotationFlags": ["CCDS", "basic"]}, {"sequenceOntologyTerms": [{"accession": "SO:0001566", "name": "regulatory_region_variant"}]}], "conservation": [{"score": 1.149999976158142, "source": "gerp"}, {"score": 0.1289999932050705, "source": "phastCons"}, {"score": -0.527999997138977, "source": "phylop"}], "cytoband": [{"chromosome": "1", "end": 2300000, "name": "p36.33", "stain": "gneg", "start": 1}], "displayConsequenceType": "missense_variant", "functionalScore": [{"score": -0.7899999618530273, "source": "cadd_raw"}, {"score": 0.03999999910593033, "source": "cadd_scaled"}], "geneDrugInteraction": [], "geneTraitAssociation": [], "hgvs": ["ENST00000335137(ENSG00000186092):c.421A>G"], "id": "rs2691305", "populationFrequencies": [{"altAllele": "G", "altAlleleFreq": 0.95061594, "altHomGenotypeFreq": 0.93263996, "hetGenotypeFreq": 0.03595196, "population": "ALL", "refAllele": "A", "refAlleleFreq": 0.049384065, "refHomGenotypeFreq": 0.031408086, "study": "GNOMAD_EXOMES"}, {"altAllele": "G", "altAlleleFreq": 0.9499386, "altHomGenotypeFreq": 0.92997545, "hetGenotypeFreq": 0.03992629, "population": "OTH", "refAllele": "A", "refAlleleFreq": 0.050061423, "refHomGenotypeFreq": 0.03009828, "study": "GNOMAD_EXOMES"}, {"altAllele": "G", "altAlleleFreq": 0.999461, "altHomGenotypeFreq": 0.99892205, "hetGenotypeFreq": 0.0010779734, "population": "EAS", "refAllele": "A", "refAlleleFreq": 0.0005389867, "refHomGenotypeFreq": 0.0, "study": "GNOMAD_EXOMES"}, {"altAllele": "G", "altAlleleFreq": 0.95083994, "altHomGenotypeFreq": 0.9305369, "hetGenotypeFreq": 0.040606, "population": "AMR", "refAllele": "A", "refAlleleFreq": 0.049160052, "refHomGenotypeFreq": 0.028857054, "study": "GNOMAD_EXOMES"}, {"altAllele": "G", "altAlleleFreq": 0.97795016, "altHomGenotypeFreq": 0.9710086, "hetGenotypeFreq": 0.013883217, "population": "ASJ", "refAllele": "A", "refAlleleFreq": 0.022049816, "refHomGenotypeFreq": 0.015108207, "study": "GNOMAD_EXOMES"}, {"altAllele": "G", "altAlleleFreq": 0.99145377, "altHomGenotypeFreq": 0.98848504, "hetGenotypeFreq": 0.0059373877, "population": "FIN", "refAllele": "A", "refAlleleFreq": 0.00854624, "refHomGenotypeFreq": 0.005577546, "study": "GNOMAD_EXOMES"}, {"altAllele": "G", "altAlleleFreq": 0.9727796, "altHomGenotypeFreq": 0.96255124, "hetGenotypeFreq": 0.020456737, "population": "NFE", "refAllele": "A", "refAlleleFreq": 0.027220415, "refHomGenotypeFreq": 0.016992046, "study": "GNOMAD_EXOMES"}, {"altAllele": "G", "altAlleleFreq": 0.6074365, "altHomGenotypeFreq": 0.47664425, "hetGenotypeFreq": 0.26158446, "population": "AFR", "refAllele": "A", "refAlleleFreq": 0.39256352, "refHomGenotypeFreq": 0.2617713, "study": "GNOMAD_EXOMES"}, {"altAllele": "G", "altAlleleFreq": 0.95853204, "altHomGenotypeFreq": 0.94338477, "hetGenotypeFreq": 0.03029453, "population": "MALE", "refAllele": "A", "refAlleleFreq": 0.041467976, "refHomGenotypeFreq": 0.02632071, "study": "GNOMAD_EXOMES"}, {"altAllele": "G", "altAlleleFreq": 0.94091445, "altHomGenotypeFreq": 0.91947174, "hetGenotypeFreq": 0.04288538, "population": "FEMALE", "refAllele": "A", "refAlleleFreq": 0.05908557, "refHomGenotypeFreq": 0.03764288, "study": "GNOMAD_EXOMES"}, {"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": 0.9404255, "altHomGenotypeFreq": 0.9191489, "hetGenotypeFreq": 0.04255319, "population": "OTH", "refAllele": "A", "refAlleleFreq": 0.05957447, "refHomGenotypeFreq": 0.038297873, "study": "GNOMAD_GENOMES"}, {"altAllele": "G", "altAlleleFreq": 1.0, "altHomGenotypeFreq": 1.0, "hetGenotypeFreq": 0.0, "population": "EAS", "refAllele": "A", "refAlleleFreq": 0.0, "refHomGenotypeFreq": 0.0, "study": "GNOMAD_GENOMES"}, {"altAllele": "G", "altAlleleFreq": 0.9410377, "altHomGenotypeFreq": 0.9103774, "hetGenotypeFreq": 0.061320756, "population": "AMR", "refAllele": "A", "refAlleleFreq": 0.058962263, "refHomGenotypeFreq": 0.028301887, "study": "GNOMAD_GENOMES"}, {"altAllele": "G", "altAlleleFreq": 0.9672131, "altHomGenotypeFreq": 0.9508197, "hetGenotypeFreq": 0.032786883, "population": "ASJ", "refAllele": "A", "refAlleleFreq": 0.032786883, "refHomGenotypeFreq": 0.016393442, "study": "GNOMAD_GENOMES"}, {"altAllele": "G", "altAlleleFreq": 0.9918478, "altHomGenotypeFreq": 0.98913044, "hetGenotypeFreq": 0.0054347827, "population": "FIN", "refAllele": "A", "refAlleleFreq": 0.008152174, "refHomGenotypeFreq": 0.0054347827, "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"}, {"altAllele": "G", "altAlleleFreq": 0.5886525, "altHomGenotypeFreq": 0.41246733, "hetGenotypeFreq": 0.3523703, "population": "AFR", "refAllele": "A", "refAlleleFreq": 0.4113475, "refHomGenotypeFreq": 0.23516238, "study": "GNOMAD_GENOMES"}, {"altAllele": "G", "altAlleleFreq": 0.8381471, "altHomGenotypeFreq": 0.7682737, "hetGenotypeFreq": 0.13974673, "population": "MALE", "refAllele": "A", "refAlleleFreq": 0.16185293, "refHomGenotypeFreq": 0.09197956, "study": "GNOMAD_GENOMES"}, {"altAllele": "G", "altAlleleFreq": 0.84750646, "altHomGenotypeFreq": 0.78322285, "hetGenotypeFreq": 0.12856731, "population": "FEMALE", "refAllele": "A", "refAlleleFreq": 0.1524935, "refHomGenotypeFreq": 0.08820986, "study": "GNOMAD_GENOMES"}], "reference": "A", "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}], "start": 69511, "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": []}], "variantTraitAssociation": {"clinvar": [], "cosmic": [{"geneName": "OR4F5", "histologySubtype": "neoplasm", "mutationId": "COSM4144171", "mutationSomaticStatus": "Confirmed " "somatic " "variant", "primaryHistology": "other", "primarySite": "thyroid", "sampleSource": "", "siteSubtype": "", "tumourOrigin": ""}]}}}
Implementation
Variant data model is implemented in OpenCB Biodata project, this allows the resto of OpenCB projects such as CellBase, Oskar to
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