graph TD
A("Raw data(BCL format files)") --> |"de-multiplexing<--bcl2fastq"| B(FASTQ files);
%% style A fill:#63CA01,stroke:#333;
B -->|"FASTQ QC<--FastQC"| C(FASTQ QC report);
B -->|data preprocessing| D(filtered fastq);
D -->|alignment<--BWA| E(original BAM);
E -->|BAM sorting| F(sorted BAM);
F --> G(BAM QC report);
F -->|realignment deduplication| H(final BAM);
H -->|Variant calling| I(original VCF);
I -->|database annotation| J(database annotated VCF);
J -->|baseline annotation| k(baseline annotated VCF);
k -->|unique read counting| L(Complete VCF);
L -->|variant filtering| M(clean variants);
L -->|visualization| N(Visualized targets);
N -->|interactive analysis| o(clinical interpretation)
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