Index

_

__init__() (pGermlinePoly.pGermlinePoly.ClonalSim method)

B

B (pGermlinePoly.pGermlinePoly.ProbGermline attribute)

BetaOverdispersion (class in pGermlinePoly.pGermlinePoly)

C

check_annotations() (in module pGermlinePoly.io) check_samples() (in module pGermlinePoly.io) ClonalSim (class in pGermlinePoly.pGermlinePoly) complete_logll() (pGermlinePoly.pGermlinePoly.ProbGermline method)

create_anno() (in module pGermlinePoly.io) create_germline_anno() (in module pGermlinePoly.io) create_gt_string() (pGermlinePoly.pGermlinePoly.ClonalSim method) create_read_matrix() (in module pGermlinePoly.io) (pGermlinePoly.pGermlinePoly.ClonalSim method)

E

em_algo() (pGermlinePoly.pGermlinePoly.ProbGermline method) est_germline_genotype() (pGermlinePoly.pGermlinePoly.ProbGermline method)

est_germline_prior() (pGermlinePoly.pGermlinePoly.MutectLOD method) est_vaf_CI() (pGermlinePoly.pGermlinePoly.ProbGermline method) estimate_rhos() (pGermlinePoly.pGermlinePoly.BetaOverdispersion method)

I

impute_anno() (pGermlinePoly.pGermlinePoly.ProbGermline method)

J

J (pGermlinePoly.pGermlinePoly.MutectLOD attribute) (pGermlinePoly.pGermlinePoly.ProbGermline attribute)

K

kappa (pGermlinePoly.pGermlinePoly.ProbGermline attribute)

L

L (pGermlinePoly.pGermlinePoly.ProbGermline attribute) lod (pGermlinePoly.pGermlinePoly.MutectLOD attribute) lod_germline (pGermlinePoly.pGermlinePoly.MutectLOD attribute)

lod_germline() (pGermlinePoly.pGermlinePoly.MutectLOD method) lod_scores() (pGermlinePoly.pGermlinePoly.MutectLOD method) loglik_ratio_het() (pGermlinePoly.pGermlinePoly.ProbGermline method)

M

M (pGermlinePoly.pGermlinePoly.MutectLOD attribute) (pGermlinePoly.pGermlinePoly.ProbGermline attribute) mle_vaf() (pGermlinePoly.pGermlinePoly.ProbGermline method)

module pGermlinePoly.io mu (pGermlinePoly.pGermlinePoly.ProbGermline attribute) MutectLOD (class in pGermlinePoly.pGermlinePoly)

N

naive_mle() (pGermlinePoly.pGermlinePoly.ProbGermline method)

P

pGermlinePoly.io module

post_prob_poly() (pGermlinePoly.pGermlinePoly.ProbGermline method) prior_poly() (pGermlinePoly.pGermlinePoly.ProbGermline method) ProbGermline (class in pGermlinePoly.pGermlinePoly)

S

sim_somatic_mutations() (pGermlinePoly.pGermlinePoly.ClonalSim method) simulate_clonal_germline_muts() (pGermlinePoly.pGermlinePoly.ClonalSim method)

simulate_clone_genealogy() (pGermlinePoly.pGermlinePoly.ClonalSim method) simulate_germline() (pGermlinePoly.pGermlinePoly.ClonalSim method) simulate_germline_somatic_muts() (pGermlinePoly.pGermlinePoly.ClonalSim method)

V

vaf (pGermlinePoly.pGermlinePoly.ProbGermline attribute)

validate_config() (in module pGermlinePoly.io)

W

write_vcf() (pGermlinePoly.pGermlinePoly.ClonalSim method)