從 FASTQ 到臨床解讀——12 個步驟掌握 全基因組 (WGS) 與 全外顯子 (WES) 變異分析流程，搭配互動模擬與 GATK 程式碼範例。
From FASTQ to clinical interpretation — master Whole Genome (WGS) and Whole Exome (WES) variant analysis in 12 steps, with interactive simulations and GATK code examples.
理解兩種定序策略的覆蓋範圍、成本、適用情境，並選擇正確的方法。
Understand coverage, cost, and use cases of both strategies. Choose the right approach.
用 FastQC、fastp 評估 Phred 分數、adapter 含量，並進行 trimming。
Assess Phred scores and adapter content with FastQC/fastp, then trim reads.
用 BWA-MEM/MEM2 將 reads 比對到參考基因組，產出 BAM 檔。
Align reads to the reference genome with BWA-MEM/MEM2, producing BAM files.
MarkDuplicates 標記 PCR 重複，BQSR 校正鹼基品質分數。
Mark PCR duplicates and recalibrate base quality scores (BQSR).
HaplotypeCaller、DeepVariant、DRAGEN 比較與 GVCF 模式。
Compare HaplotypeCaller, DeepVariant, DRAGEN, and the GVCF workflow.
GenomicsDBImport + GenotypeGVCFs：跨樣本提升 rare variant 召回率。
GenomicsDBImport + GenotypeGVCFs: boost rare-variant recall across cohorts.
VQSR 機器學習過濾 vs 硬性閾值 (Hard Filtering)，何時用哪個？
VQSR machine-learning filtering vs hard thresholds — when to use each.
VEP、ANNOVAR、SnpEff 比較，加入 gnomAD、ClinVar 等族群與臨床資料庫。
Compare VEP, ANNOVAR, SnpEff. Layer in gnomAD, ClinVar, and population databases.
用 ACMG/AMP 五級分類系統 (Pathogenic ↔ Benign) 評估臨床意義。
Use the ACMG/AMP 5-tier system (Pathogenic ↔ Benign) to assess clinical significance.
Mutect2 tumor-vs-normal 分析、Panel of Normals、低 VAF 突變偵測。
Mutect2 tumor-vs-normal analysis, Panel of Normals, low-VAF mutation detection.
用 Manta、Delly、CNVnator 偵測 >50bp 的 deletions、duplications、translocations。
Detect >50bp deletions, duplications, and translocations with Manta, Delly, CNVnator.
target enrichment、capture kit 選擇、coverage uniformity、外顯子盲區。
Target enrichment, capture kit choice, coverage uniformity, exome blind spots.