{"title":"WGS 变异检测流程","description":"从全基因组测序 reads 到 SNV/Indel 变异集合的标准检测流程。","omics_type":"WGS","category_key":"variant","category_name":"基因组变异与定位","dag_json":{"nodes":[{"id":"qc","label":"reads 质控"},{"id":"bwa","label":"BWA-MEM 比对"},{"id":"markdup","label":"重复标记"},{"id":"bqsr","label":"BQSR 校正"},{"id":"haplotype","label":"GATK HaplotypeCaller"}],"edges":[{"source":"qc","target":"bwa"},{"source":"bwa","target":"markdup"},{"source":"markdup","target":"bqsr"},{"source":"bqsr","target":"haplotype"}]},"metadata_json":{"difficulty":"入门","tools":[],"inputs":["FASTQ","BAM","VCF"],"outputs":[],"estimated_time":"0.5-1 天","scenario":"基因组变异"},"content":"# WGS 变异检测流程\n\n## 适用场景\n适用于人类或模式物种全基因组测序数据，用于检测 SNV 与小 Indel。\n\n## 核心步骤\n1. 对原始 FASTQ 进行质量评估。\n2. 使用 BWA-MEM 将 reads 比对到参考基因组。\n3. 使用 Picard 或 GATK MarkDuplicates 标记 PCR duplicates。\n4. 使用 GATK 进行碱基质量分数重校正。\n5. 使用 HaplotypeCaller 生成样本级 GVCF，并进行联合分型。\n\n## 主要输出\n- 排序后的 BAM 文件\n- 变异检测 VCF\n- 变异质控统计\n- 可进入注释环节的候选变异集合\n","id":21,"created_at":"2026-06-03T17:48:59.764103Z"}