cfDNA coverage bias

Analysis of sequencing coverage bias in cfDNA relative to matched tumor data from targeted sequencing.

Overview

This repository contains code and example data for analyzing locus-specific sequencing coverage bias in cell-free DNA (cfDNA) compared with tumor sequencing data from targeted panels. The project focuses on identifying under-represented and over-represented genomic positions in cfDNA and assessing their potential clinical relevance.

Repository structure

input_data/
├── example_underrepresent_cohort/   # example input files for reproducing core analyses
├── data/                            # contain allele-specific power calculations for different VAF
scripts/                             # analysis and preprocessing scripts
results/                             # output tables, figures, and summary files