{"id":"JGAD000868","research":"hum0014","url":"https://humandbs.dbcls.jp/dataset/JGAD000868","datePublished":"2024-08-28","dateModified":"2024-08-28","values":[{"key":"access-criteria","label":{"ja":"アクセス制限","en":"Access criteria"},"type":"vocabulary","terms":[{"code":"controlled-access-type-1","label":{"ja":"制限公開（Type I）","en":"Controlled-access (Type I)"}}]},{"key":"type-of-data","label":{"ja":"データの種類","en":"Type of data"},"type":"text","text":{"ja":"JGAD000495（バイオバンクジャパン1,964名のWGSデータ）の加工データ（TogoImputation用reference panelデータ）","en":"Processed data of JGAD000495 (reference panel) by JGA (data for the TogoImputation reference panel)"}}],"experiments":[{"label":{"ja":"WGS インピュテーションパネル (autosomes + X)","en":"WGS imputation panel (autosomes + X)"},"values":[{"key":"materials-and-participants","label":{"ja":"材料と対象者","en":"Materials and participants"},"type":"text","text":{"ja":"バイオバンクジャパン1,964名のWGSデータ(JGAD000495)のvcfファイル(WGSデータの分子データは上記参照のこと)","en":"WGS data (JGAD000495) of the biobank Japan project (N=1,964)"}},{"key":"subject-count","label":{"ja":"対象者数","en":"Subject count"},"type":"number","numbers":[{"value":2990,"unit":null,"high":null}]},{"key":"subject-count-type","label":{"ja":"対象者数の数え方","en":"Counted as"},"type":"vocabulary","terms":[{"code":"individual","label":{"ja":"人数","en":"Individual"}}]},{"key":"cohort","label":{"ja":"コホート","en":"Cohort"},"type":"vocabulary","terms":[{"code":"biobank-japan","label":{"en":"BioBank Japan"}}]},{"key":"experimental-method","label":{"ja":"実験方法","en":"Experimental method"},"type":"vocabulary","terms":[{"code":"wgs","label":{"en":"WGS"}}]},{"key":"targets","label":{"ja":"測定対象","en":"Target"},"type":"text","text":{"ja":null,"en":null}},{"key":"reference-sequence","label":{"ja":"参照ゲノム","en":"Reference genome"},"type":"vocabulary","terms":[{"code":"grch38","label":{"en":"GRCh38"}}]},{"key":"mapping","label":{"ja":"マッピング","en":"Mapping"},"type":"text","text":{"ja":"bwa mem（version 0.7.15）","en":"bwa mem (version 0.7.15)"}},{"key":"read-deduplication","label":{"ja":"リード重複除去","en":"Read deduplication"},"type":"text","text":{"ja":"GATK MarkDuplicates（version 4.1.0.0）","en":"GATK MarkDuplicates (version 4.1.0.0)"}},{"key":"calibration-for-re-alignment-and-base-quality","label":{"ja":"再アライメント・塩基品質補正","en":"Realignment and base quality recalibration"},"type":"text","text":{"ja":null,"en":null}},{"key":"mapping-quality","label":{"ja":"マッピング品質","en":"Mapping quality"},"type":"text","text":{"ja":null,"en":null}},{"key":"filtering","label":{"ja":"QC・フィルタリング","en":"QC and filtering"},"type":"text","text":{"ja":"生殖系列（germline）の全ゲノムシークエンスデータの加工を行い、aggregate VCFを計算した。その後、下記の条件でvariantsのフィルタリングを行った。\n(1) VQSRフィルタを通過しなかったvariantsの除外\n(2) Multi-allelic sitesの除外\n(3) Call rate が低い（95%未満）variantsの除外\n(4) Hardy-Weinberg平衡から逸脱している（P<1e-10）variantsの除外\n(5) Minor allele count（MAC）が小さい（< 2）variantsの除外","en":"Germline whole genome sequencing data were processed, and the aggregate VCF was calculated. Variants were then filtered based on the following conditions:\n(1) Variants that did not pass the VQSR filter were excluded\n(2) Multi-allelic sites were excluded\n(3) Variants with a call rate below 95% were excluded\n(4) Variants deviating from Hardy-Weinberg equilibrium (P < 1e-10) were excluded\n(5) Variants with a minor allele count (MAC) less than 2 were excluded"}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"GATK HaplotypeCaller -ERC GVCF（version 4.1.0.0）\nバリアント検出時のパラメータである ploidy は次のように設定した。\n常染色体および pseudoautosomal region（PAR） 領域：ploidy=2\nX染色体のnon-PAR領域：ploidy=2（女性） および ploidy=1（男性）\nY染色体の non-PAR 領域：ploidy=1（男性）","en":"GATK HaplotypeCaller -ERC GVCF (version 4.1.0.0)\nThe ploidy for variant call was set as follows:\nAutosomes and pseudoautosomal regions (PARs): ploidy=2\nNon-PARs on the X chromosome: ploidy=2 (female) and ploidy=1 (male)\nNon-PARs on the Y chromosome: ploidy=1 (male)"}},{"key":"coverage-depth","label":{"ja":"カバレッジ (深度)","en":"Coverage (depth)"},"type":"number","numbers":[{"value":19.61,"unit":"x","high":null,"suffix":{"ja":" (± 5.41)","en":" (± 5.41)"}}]},{"key":"variant-number","label":{"ja":"バリアント数","en":"Variant count"},"type":"number","numbers":[{"value":21596248,"unit":null,"high":null,"suffix":{"ja":" variants","en":" variants"}},{"value":21157732,"unit":null,"high":null,"prefix":{"ja":"常染色体: ","en":"Autosomes: "},"suffix":{"ja":" variants","en":" variants"}},{"value":438516,"unit":null,"high":null,"prefix":{"ja":"X染色体: ","en":"X chromosome: "},"suffix":{"ja":" variants","en":" variants"}}]},{"key":"processed-data-type","label":{"ja":"加工データの種類","en":"Processed data type"},"type":"vocabulary","terms":[{"code":"reference-panel","label":{"ja":"リファレンスパネル","en":"Reference panel"}},{"code":"variant-calls","label":{"ja":"変異コール","en":"Variant calls"}}]},{"key":"original-data-dataset-id","label":{"ja":"元データのデータセットID","en":"Dataset ID of original data"},"type":"text","text":{"ja":"JGAD000220\nJGAD000495","en":"JGAD000220\nJGAD000495"}},{"key":"processing-method","label":{"ja":"加工方法","en":"Processing method"},"type":"text","text":{"ja":"加工済みデータ一覧（Imputation reference）","en":"List of processed data (Imputation reference)"}},{"key":"policies","label":{"ja":"利用ポリシー","en":"Data use policy"},"type":"vocabulary","terms":[{"code":"nbdc-data-sharing-policy-jgap000001","label":{"ja":"NBDC データ共有ポリシー (JGAP000001)","en":"NBDC data sharing policy (JGAP000001)"}}]}]}],"dataVolume":6208834582,"fileFormats":[{"code":"tar","label":{"en":"TAR"}}]}