Welcome to pGermlinePoly’s documentation!

pGermlinePoly is a Bayesian model to estimate the posterior probability of germline polymorphism in somatic sequencing data. Annotation weights — capturing how features such as population allele frequency or sequencing depth inform the germline prior — are learned directly from the data via empirical Bayes rather than specified by the user. The underlying EM algorithm jointly estimates these logistic annotation weights and a Beta-Binomial error concentration parameter, enabling data-driven discrimination between germline heterozygotes and somatic variants.

Beyond the primary EM-based classifier, pGermlinePoly also provides general-purpose tools for somatic variant filtering: a frequentist likelihood ratio test (--lrt), a Mutect2 LOD score (--mutect2), and a Beta-Binomial overdispersion statistic (--betabinomial). The tool is designed to annotate somatic VCFs in-place — all scores are written directly to the INFO fields of the input VCF — making it straightforward to integrate into existing somatic variant calling pipelines.

Contents:

• pGermlinePoly API Reference
  • Inference
    • ProbGermline
      • ProbGermline.impute_anno()
      • ProbGermline.reflect_af_annotations()
      • ProbGermline.mle_vaf()
      • ProbGermline.loglik_ratio_het()
      • ProbGermline.prior_poly()
      • ProbGermline.post_prob_poly()
      • ProbGermline.est_vaf_CI()
      • ProbGermline.est_germline_genotype()
      • ProbGermline.complete_logll()
      • ProbGermline.naive_mle()
      • ProbGermline.m_step_lambda_beta()
      • ProbGermline.em_algo()
    • MutectLOD
      • MutectLOD.lod_scores()
      • MutectLOD.est_germline_prior()
      • MutectLOD.lod_germline()
    • BetaOverdispersion
      • BetaOverdispersion.estimate_rhos()
  • Simulation
    • ClonalSim
      • ClonalSim.__init__()
      • ClonalSim.simulate_germline()
      • ClonalSim.simulate_clone_genealogy()
      • ClonalSim.sim_somatic_mutations()
      • ClonalSim.simulate_clonal_germline_muts()
      • ClonalSim.simulate_germline_somatic_muts()
      • ClonalSim.create_read_matrix()
      • ClonalSim.create_gt_string()
      • ClonalSim.write_vcf()
  • I/O Utilities
    • parse_annotation()
    • is_af_annotation()
    • annotation_transform_name()
    • validate_config()
    • check_samples()
    • check_annotations()
    • create_germline_anno()
    • create_anno()
    • create_read_matrix()

Indices and tables

• Index

• Module Index

• Search Page