bio-liquid-biopsy-pipeline

What problem does it solve?

This pipeline provides an end-to-end workflow for analyzing plasma-derived cfDNA, enabling tumor fraction estimation, mutation detection, and longitudinal monitoring from sequencing data.

Core Features & Use Cases

• Preprocess cfDNA with UMI-aware deduplication: prepares high-quality input by collapsing reads with UMIs to reduce collateral errors.
• Fragment QC & cfDNA profiling: performs fragment-size analysis to verify cfDNA quality and detect characteristic mono-/di-nucleosome patterns.
• Tumor fraction estimation (sWGS) with ichorCNA: estimates tumor fraction from shallow whole-genome sequencing data.
• Mutation detection for targeted panels: calls somatic variants from deep targeted sequencing and applies CHIP filtering.
• Longitudinal tracking: analyzes serial samples to monitor ctDNA dynamics over time.
• Use Case: Researchers can run this pipeline to monitor treatment response via serial tumor fraction and mutation burden.

Quick Start

Invoke run_liquid_biopsy_pipeline with a sample_config detailing bam_file, data_type, reference, bed_file (if panel), and output_dir to execute the full workflow.