This repository contains the code, data, and documentation for analyses involving the CEPH 1463 pedigree.
This folder includes Snakemake files used to generate the truth sets, covering both small variants and structural variants (SVs).
This folder contains README files detailing the various analyses performed:
- Pedigree filtering: Concordance analysis code.
- De novo mutation discovery: Analysis for Porubsky et al., 2024.
- High Confidence Regions (HCR): Definition and selection of HCR for the truth set.
- Rust: Source code for the toolkit (an ensemble of binaries).
- Python: Source code for various analyses, including SV merging.