heredicalc 4.1.0

Full Likelihood Bayes factor computation for hereditary cosegregation analysis

HerediCalc v4

Full Likelihood Bayes (FLB) factor computation for Bayesian cosegregation analysis.

HerediCalc quantifies whether a genetic entity co-segregates with a heritable phenotype in a pedigree beyond what is expected by chance. The resulting FLB factor supports pathogenicity classification of genetic variants (FLB > 10: strong evidence of pathogenicity).

Requirements

• Python ≥ 3.12
• R ≥ 4.2 with packages: segregatr, kinship2

Quick Install

pip install heredicalc

For R dependency setup, see the documentation.

Quick Start

# Generate a config file interactively
heredicalc add config

# Run FLB computation
heredicalc run Belman.ped --config heredicalc.yml

# Batch computation over a directory of pedigrees
heredicalc batch pedigrees/ --config heredicalc.yml

Example heredicalc.yml:

computation:
  genetic_entity: BRCA1
  allele_freq: 0.0001

plugins:
  incidence_source: ci5_ix
  phenotype_model: hbopc
  trait_mapper: ci5_ix_hbopc
  penetrance_model: victor
  flb_calculator: segregatr
  params:
    population: Latvia
    age_bands: [30, 40, 50, 60, 65, 70, 80]

Documentation

Full documentation: https://heredicalc.github.io/heredicalc

Contributing

See CONTRIBUTING.md.

License

MIT