Welcome to pGermlinePoly’s documentation!

pGermlinePoly is a Bayesian model to estimate the posterior probability of germline polymorphism in somatic sequencing data. It implements an EM algorithm that jointly estimates logistic annotation weights and a Beta-Binomial error concentration to discriminate germline heterozygotes from somatic variants.

Contents:

• pGermlinePoly API Reference
  • Inference
    • ProbGermline
      • ProbGermline.M
      • ProbGermline.J
      • ProbGermline.L
      • ProbGermline.B
      • ProbGermline.kappa
      • ProbGermline.mu
      • ProbGermline.vaf
      • ProbGermline.impute_anno()
      • 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.em_algo()
    • MutectLOD
      • MutectLOD.M
      • MutectLOD.J
      • MutectLOD.lod
      • MutectLOD.lod_germline
      • 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
    • validate_config()
    • check_samples()
    • check_annotations()
    • create_germline_anno()
    • create_anno()
    • create_read_matrix()

Indices and tables

• Index

• Module Index

• Search Page