{"id":"JGAD000679","research":"hum0014","url":"https://humandbs.dbcls.jp/dataset/JGAD000679","datePublished":"2023-01-26","dateModified":"2023-01-26","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":"JGAD000220（reference panel）の加工データ（TogoImputation用reference panelデータ）","en":"Processed data of JGAD000220 (reference panel) by JGA (data for the TogoImputation reference panel)"}}],"experiments":[{"label":{"ja":"WGS リファレンスパネル (autosomes + X)","en":"WGS reference panel (autosomes + X)"},"values":[{"key":"subject-count","label":{"ja":"対象者数","en":"Subject count"},"type":"number","numbers":[{"value":1037,"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"}},{"code":"1000-genomes-project","label":{"en":"1000 Genomes Project"}}]},{"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":"grch37","label":{"en":"GRCh37"}}]},{"key":"mapping","label":{"ja":"マッピング","en":"Mapping"},"type":"text","text":{"ja":"BWA-MEM (version 0.7.5a)","en":"BWA-MEM (version 0.7.5a)"}},{"key":"read-deduplication","label":{"ja":"リード重複除去","en":"Read deduplication"},"type":"text","text":{"ja":"picard (versions 1.106)","en":"picard (versions 1.106)"}},{"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":"GATK (version 3.2-2)","en":"GATK (ver.3.2-2)"}},{"key":"mapping-quality","label":{"ja":"マッピング品質","en":"Mapping quality"},"type":"text","text":{"ja":"MAPQ < 20 を除外（HaplotypeCaller）","en":"MAPQ < 20 were excluded (HaplotypeCaller)"}},{"key":"filtering","label":{"ja":"QC・フィルタリング","en":"QC and filtering"},"type":"text","text":{"ja":"We set exclusion criteria for genotypes as follows:\n(1) DP < 5, (2) GQ < 20, or (3) DP > 60 and GQ < 95, and regarded these genotypes as missing.\nVariants with call rates < 90% were excluded before variant quality score recalibration (VQSR).\nAfter VQSR, we excluded variants located in low-complexity regions (LCR), as defined by mdust software were excluded.\nFinally, we used BEAGLE to impute missing genotypes.","en":"We set exclusion criteria for genotypes as follows:\n(1) DP < 5, (2) GQ < 20, or (3) DP > 60 and GQ < 95, and regarded these genotypes as missing.\nVariants with call rates < 90% were excluded before variant quality score recalibration (VQSR).\nAfter VQSR, we excluded variants located in low-complexity regions (LCR), as defined by mdust software were excluded.\nFinally, we used BEAGLE to impute missing genotypes."}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"GATK HaplotypeCaller (version 3.2-2)","en":"GATK HaplotypeCaller (version 3.2-2)"}},{"key":"coverage-depth","label":{"ja":"カバレッジ (深度)","en":"Coverage (depth)"},"type":"number","numbers":[{"value":30,"unit":"x","high":null,"suffix":{"ja":" (目標深度)","en":" (aimed at depth)"}}]},{"key":"variant-number","label":{"ja":"バリアント数","en":"Variant count"},"type":"number","numbers":[{"value":61608817,"unit":null,"high":null,"suffix":{"ja":" variants","en":" variants"}},{"value":59387070,"unit":null,"high":null,"prefix":{"ja":"常染色体: ","en":"Autosomes: "},"suffix":{"ja":" variants","en":" variants"}},{"value":2221747,"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","en":"JGAD000220"}},{"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":33318625280,"fileFormats":[{"code":"tar","label":{"en":"TAR"}}]}