bio-tumor-fraction-estimation - Estimate tumor fraction from cfDNA sequencing
Estimates genome-wide tumor fraction from cfDNA, primarily using ichorCNA for shallow whole-genome sequencing and selecting alternatives by assay type.
Tags
Updated: 2026-09-29Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Estimate tumor fraction
- Bin BAM coverage
- Run ichorCNA HMM
- Parse ichorCNA results
- Inspect copy-number plots
- Compare TF with VAF
- Select assay-specific estimators
Inputs
- cfDNA BAM file
- Assay type
- Reference genome build
- GC and mappability WIG files
- Centromere reference
- Panel-of-normals file
- Targeted variant data
- Methylation data
Outputs
- Tumor fraction estimate
- Tumor ploidy estimate
- Copy-number segments
- ichorCNA parameter file
- Genome-wide plot
- Quality-control metrics
- Estimator recommendation
Requirements
- R 4.2+
- ichorCNA 0.6.0+
- HMMcopy 1.40+
- Rscript command-line access
- GavinHaLab ichorCNA fork
- Build-matched reference files
- Protocol-matched panel of normals