bio-workflows-liquid-biopsy-pipeline - Orchestrate an end-to-end liquid biopsy pipeline
Orchestrates cfDNA and liquid-biopsy analysis from pre-analytic QC and UMI consensus through tumor fraction, mutation detection, optional fragmentomics or methylation, and longitudinal monitoring.
Tags
Updated: 2026-10-12Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Check pre-analytic quality
- Build UMI consensus reads
- Assess cfDNA fragments
- Estimate tumor fraction
- Detect low-VAF mutations
- Subtract matched-WBC CHIP
- Analyze fragmentomics and methylation
- Track longitudinal responses
Inputs
- cfDNA sequencing data
- Sample metadata
- Matched WBC sequencing data
- Assay design
- Reference genome
- Longitudinal sample series
Outputs
- QC metrics
- Consensus BAM files
- Tumor fraction estimates
- Somatic mutation calls
- Fragmentomics results
- Methylation results
- Longitudinal monitoring results
Requirements
- BWA 0.7.17 or later
- fgbio 2.1 or later
- ichorCNA 0.6.0 or later
- VarDict 1.8 or later
- FinaleToolkit 0.9 or later
- MethylDackel 0.6 or later
- Python and R environments
- Reference genome
- Component liquid-biopsy skills