bio-workflows-liquid-biopsy-pipeline

Orchestrates the cell-free DNA / liquid-biopsy pipeline from plasma sequencing to tumor monitoring, forking tumor-naive (screening) vs tumor-informed (MRD), and chaining pre-analytic QC, UMI/duplex error-suppression (fgbio), fragment QC, ichorCNA tumor fraction (sWGS) or VarDict low-VAF calling (panel), CHIP subtraction against matched WBC, optional fragmentomics/methylation, and longitudinal tracking. Use when treating pre-analytics as the irreversible sensitivity ceiling (tube/time-to-plasma/hemolysis), running error-suppression BEFORE calling (single-strand consensus does not remove deamination; only duplex does), reporting a VAF only with input genome-equivalents (TF ~ 2x VAF only for clonal-het-diploid), subtracting CHIP before reporting somatic, or keeping tube/panel/pipeline identical across a longitudinal MRD series. Hands mechanism to the liquid-biopsy component skills; not a re-teach of any single step.