ancIBD
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Contents:
Overview
Installation
Preparing Input for ancIBD: VCF->HDF5
Vignette: Calling IBD with ancIBD
Vignette: Visualize ancIBD output
Running ancIBD via bash
Running ancIBD on X chromosomes (available from ancIBD v0.6)
Detecting IBD2 (available from ancIBD v0.6)
Frequently Asked Questions (FAQ)
API Reference
ancIBD
Index
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Index
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B
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C
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E
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F
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G
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H
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I
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J
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L
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M
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N
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O
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P
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R
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S
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T
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V
A
all_pairs_ibd() (in module ancIBD.IO.ind_ibd)
ancIBD
module
ancIBD.ancIBD_summary
module
ancIBD.emission
module
ancIBD.hmm
module
ancIBD.ibd_stats
module
ancIBD.ibd_stats.funcs
module
ancIBD.IO
module
ancIBD.IO.batch_run
module
ancIBD.IO.h5_duplicates
module
ancIBD.IO.h5_load
module
ancIBD.IO.h5_modify
module
ancIBD.IO.h5_qc
module
ancIBD.IO.ind_ibd
module
ancIBD.IO.prepare_h5
module
ancIBD.loaddata
module
ancIBD.main
module
ancIBD.plot
module
ancIBD.plot.plot_df
module
ancIBD.plot.plot_karyotype
module
ancIBD.plot.plot_opphomos
module
ancIBD.plot.plot_posterior
module
ancIBD.postprocessing
module
ancIBD.run
module
ancIBD.run_ancIBD
module
ancIBD.run_ancIBDX
module
ancIBD.transition
module
B
bctools_filter_vcf() (in module ancIBD.IO.prepare_h5)
bctools_filter_vcf_allvariants() (in module ancIBD.IO.prepare_h5)
C
calc_transition_rate() (ancIBD.transition.FiveStateAsymmetric method)
(ancIBD.transition.FiveStateTransitions method)
(ancIBD.transition.FiveStatGeneric method)
(ancIBD.transition.SevenStateTransitions method)
(ancIBD.transition.ThreeStateTransitions method)
(ancIBD.transition.Transitions method)
(ancIBD.transition.TwoStateTransitions method)
call_roh() (ancIBD.postprocessing.IBD2Postprocessing method)
(ancIBD.postprocessing.NoPostProcessing method)
(ancIBD.postprocessing.PostProcessing method)
ch (ancIBD.loaddata.LoadH5Multi2 attribute)
(ancIBD.loaddata.LoadHDF5 attribute)
(ancIBD.loaddata.LoadHDF5Multi attribute)
(ancIBD.postprocessing.PostProcessing attribute)
check_valid_data() (ancIBD.loaddata.LoadData method)
chrom_length() (in module ancIBD.plot.plot_karyotype)
clean_double() (in module ancIBD.IO.batch_run)
coal_prob() (in module ancIBD.plot.plot_karyotype)
combine_all_chroms() (in module ancIBD.IO.ind_ibd)
create_df() (ancIBD.postprocessing.IBD2Postprocessing method)
(ancIBD.postprocessing.PostProcessing method)
create_ibd_pop_pair_df() (in module ancIBD.ibd_stats.funcs)
create_ind_ibd_df() (in module ancIBD.IO.ind_ibd)
create_ind_ibd_df_IBD2() (in module ancIBD.IO.ind_ibd)
create_savepath() (in module ancIBD.IO.batch_run)
cutoff_post (ancIBD.postprocessing.PostProcessing attribute)
cutoff_post1 (ancIBD.postprocessing.IBD2Postprocessing attribute)
cutoff_post2 (ancIBD.postprocessing.IBD2Postprocessing attribute)
E
e_model (ancIBD.main.HMM_Full attribute)
Emissions (class in ancIBD.emission)
exp_blocks_full_individual() (in module ancIBD.plot.plot_karyotype)
expected_block_pdf() (in module ancIBD.plot.plot_karyotype)
expected_block_pdf_chromosomes() (in module ancIBD.plot.plot_karyotype)
exponentiate_r() (ancIBD.transition.FiveStateTransitions method)
(ancIBD.transition.SevenStateTransitions method)
F
filter_ibd_df() (in module ancIBD.IO.ind_ibd)
filter_valid_data() (ancIBD.loaddata.LoadHDF5Multi method)
find_output_missing() (in module ancIBD.IO.batch_run)
find_relatives() (in module ancIBD.ibd_stats.funcs)
FiveStateAsymmetric (class in ancIBD.transition)
FiveStateTransitions (class in ancIBD.transition)
FiveStatGeneric (class in ancIBD.transition)
folder (ancIBD.postprocessing.PostProcessing attribute)
folder_in (ancIBD.main.HMM_Full attribute)
folder_out (ancIBD.main.HMM_Full attribute)
full_transition_matrix() (ancIBD.transition.FiveStateAsymmetric method)
(ancIBD.transition.FiveStateTransitions method)
(ancIBD.transition.FiveStatGeneric method)
(ancIBD.transition.SevenStateTransitions method)
(ancIBD.transition.ThreeStateTransitions method)
(ancIBD.transition.TwoStateTransitions method)
fwd_bkwd_p() (in module ancIBD.hmm)
fwd_bwd (ancIBD.main.HMM_Full attribute)
G
get_af() (in module ancIBD.IO.h5_modify)
get_af1000G() (in module ancIBD.IO.h5_modify)
get_batch_idcs() (in module ancIBD.IO.batch_run)
get_batch_nr() (in module ancIBD.IO.batch_run)
get_batch_pair_idx() (in module ancIBD.IO.batch_run)
get_ci_counts() (in module ancIBD.ibd_stats.funcs)
get_coverage() (in module ancIBD.IO.h5_load)
get_diff_gt_f() (in module ancIBD.IO.h5_load)
get_exact_idx_iid() (in module ancIBD.IO.h5_duplicates)
get_fraction_identical() (in module ancIBD.IO.h5_duplicates)
get_genos() (in module ancIBD.IO.h5_load)
get_genos_pairs() (in module ancIBD.IO.h5_load)
get_gp_df() (in module ancIBD.IO.h5_qc)
get_haplo_prob() (ancIBD.loaddata.LoadH5Multi2 method)
(ancIBD.loaddata.LoadHDF5 method)
(ancIBD.loaddata.LoadHDF5Multi method)
get_IBD_stats() (in module ancIBD.ibd_stats.funcs)
get_IBD_stats_pops() (in module ancIBD.ibd_stats.funcs)
get_idx_batch() (in module ancIBD.IO.batch_run)
get_idx_iid() (in module ancIBD.IO.h5_load)
get_idx_iid_exact() (in module ancIBD.IO.h5_load)
get_iids() (in module ancIBD.IO.batch_run)
get_individual_idx() (ancIBD.loaddata.LoadHDF5 method)
get_map() (in module ancIBD.plot.plot_posterior)
get_markers_good() (in module ancIBD.IO.h5_duplicates)
(in module ancIBD.IO.h5_load)
get_match_df() (in module ancIBD.IO.h5_duplicates)
get_opp_homos_f() (in module ancIBD.IO.h5_load)
get_opp_homos_X() (in module ancIBD.IO.h5_load)
get_p() (ancIBD.loaddata.LoadHDF5Multi method)
get_p_hdf5() (ancIBD.loaddata.LoadHDF5Multi method)
get_posterior() (ancIBD.postprocessing.IBD2Postprocessing method)
get_run_lists_batch() (in module ancIBD.IO.batch_run)
get_run_params_from_i() (in module ancIBD.IO.batch_run)
get_sample_index() (in module ancIBD.run)
get_unique_iid_pairs() (in module ancIBD.IO.batch_run)
give_emission_log() (ancIBD.emission.Emissions method)
give_emission_matrix() (ancIBD.emission.Emissions method)
(ancIBD.emission.HaplotypeSharing_hapVSdiploid method)
(ancIBD.emission.HaplotypeSharing_twoHaploid method)
(ancIBD.emission.HaplotypeSharingEmissions method)
(ancIBD.emission.HaplotypeSharingEmissions2 method)
(ancIBD.emission.HaplotypeSharingEmissions3 method)
give_stats_cm_bin() (in module ancIBD.ibd_stats.funcs)
give_sub_df() (in module ancIBD.ibd_stats.funcs)
give_transition_rate() (ancIBD.transition.Transitions method)
H
h_model (ancIBD.main.HMM_Full attribute)
hapBLOCK_chrom() (in module ancIBD.run)
hapBLOCK_chrom_mixedPloidy() (in module ancIBD.run)
hapBLOCK_chroms() (in module ancIBD.run)
hapBLOCK_chroms_mixedPloidy() (in module ancIBD.run)
hapBLOCK_times() (in module ancIBD.run)
HaplotypeSharing_hapVSdiploid (class in ancIBD.emission)
HaplotypeSharing_twoHaploid (class in ancIBD.emission)
HaplotypeSharingEmissions (class in ancIBD.emission)
HaplotypeSharingEmissions2 (class in ancIBD.emission)
HaplotypeSharingEmissions3 (class in ancIBD.emission)
HMM_Full (class in ancIBD.main)
hw_prob_haplo_pp() (ancIBD.emission.HaplotypeSharingEmissions method)
hw_prob_haplo_share_pp() (ancIBD.emission.HaplotypeSharingEmissions method)
(ancIBD.emission.HaplotypeSharingEmissions2 method)
hw_prob_haplos_pp() (ancIBD.emission.HaplotypeSharingEmissions method)
hw_probs_shared() (ancIBD.emission.HaplotypeSharingEmissions method)
(ancIBD.emission.HaplotypeSharingEmissions2 method)
I
IBD2Postprocessing (class in ancIBD.postprocessing)
ibd_in (ancIBD.transition.FiveStateAsymmetric attribute)
(ancIBD.transition.FiveStateTransitions attribute)
(ancIBD.transition.FiveStatGeneric attribute)
(ancIBD.transition.SevenStateTransitions attribute)
(ancIBD.transition.ThreeStateTransitions attribute)
(ancIBD.transition.TwoStateTransitions attribute)
ibd_jump (ancIBD.transition.FiveStateAsymmetric attribute)
(ancIBD.transition.FiveStateTransitions attribute)
(ancIBD.transition.FiveStatGeneric attribute)
(ancIBD.transition.SevenStateTransitions attribute)
(ancIBD.transition.ThreeStateTransitions attribute)
ibd_jump2 (ancIBD.transition.FiveStateAsymmetric attribute)
ibd_lengths() (in module ancIBD.IO.ind_ibd)
ibd_out (ancIBD.transition.FiveStateAsymmetric attribute)
(ancIBD.transition.FiveStateTransitions attribute)
(ancIBD.transition.FiveStatGeneric attribute)
(ancIBD.transition.SevenStateTransitions attribute)
(ancIBD.transition.ThreeStateTransitions attribute)
(ancIBD.transition.TwoStateTransitions attribute)
ibd_stat_to_block() (ancIBD.postprocessing.PostProcessing method)
ibd_stats_pop_pairs() (in module ancIBD.ibd_stats.funcs)
iid (ancIBD.postprocessing.PostProcessing attribute)
iids (ancIBD.loaddata.LoadH5Multi2 attribute)
(ancIBD.loaddata.LoadHDF5 attribute)
(ancIBD.loaddata.LoadHDF5Multi attribute)
in_val (ancIBD.main.HMM_Full attribute)
ind_all_ibd_df() (in module ancIBD.IO.ind_ibd)
J
join_chromosomes() (in module ancIBD.IO.batch_run)
L
l_model (ancIBD.main.HMM_Full attribute)
lift_af() (in module ancIBD.IO.h5_modify)
lift_af_df() (in module ancIBD.IO.h5_modify)
load_all_data() (ancIBD.loaddata.LoadData method)
(ancIBD.loaddata.LoadHDF5 method)
(ancIBD.loaddata.LoadHDF5Multi method)
(ancIBD.loaddata.LoadSimulated method)
load_bad_areas() (in module ancIBD.plot.plot_karyotype)
load_emission_model() (in module ancIBD.emission)
load_fwd_bwd_func() (in module ancIBD.hmm)
load_individual_h5() (in module ancIBD.IO.h5_load)
load_loaddata() (in module ancIBD.loaddata)
load_objects() (ancIBD.main.HMM_Full method)
load_Postprocessing() (in module ancIBD.postprocessing)
load_transition_model() (in module ancIBD.transition)
LoadData (class in ancIBD.loaddata)
LoadH5Multi2 (class in ancIBD.loaddata)
LoadHDF5 (class in ancIBD.loaddata)
LoadHDF5Multi (class in ancIBD.loaddata)
LoadSimulated (class in ancIBD.loaddata)
M
main() (in module ancIBD.ancIBD_summary)
(in module ancIBD.run_ancIBD)
(in module ancIBD.run_ancIBDX)
mask (ancIBD.postprocessing.PostProcessing attribute)
mask_regions() (ancIBD.postprocessing.PostProcessing method)
max_gap (ancIBD.postprocessing.PostProcessing attribute)
(ancIBD.transition.FiveStateTransitions attribute)
merge_called_blocks() (ancIBD.postprocessing.PostProcessing method)
merge_in_af() (in module ancIBD.IO.h5_modify)
merge_in_ld_map() (in module ancIBD.IO.h5_modify)
merge_vcfs() (in module ancIBD.IO.prepare_h5)
min_cm (ancIBD.postprocessing.PostProcessing attribute)
min_cm2_after_merge (ancIBD.postprocessing.IBD2Postprocessing attribute)
min_cm2_init (ancIBD.postprocessing.IBD2Postprocessing attribute)
min_error (ancIBD.loaddata.LoadH5Multi2 attribute)
(ancIBD.loaddata.LoadHDF5 attribute)
(ancIBD.loaddata.LoadHDF5Multi attribute)
min_gap (ancIBD.transition.FiveStateTransitions attribute)
module
ancIBD
ancIBD.ancIBD_summary
ancIBD.emission
ancIBD.hmm
ancIBD.ibd_stats
ancIBD.ibd_stats.funcs
ancIBD.IO
ancIBD.IO.batch_run
ancIBD.IO.h5_duplicates
ancIBD.IO.h5_load
ancIBD.IO.h5_modify
ancIBD.IO.h5_qc
ancIBD.IO.ind_ibd
ancIBD.IO.prepare_h5
ancIBD.loaddata
ancIBD.main
ancIBD.plot
ancIBD.plot.plot_df
ancIBD.plot.plot_karyotype
ancIBD.plot.plot_opphomos
ancIBD.plot.plot_posterior
ancIBD.postprocessing
ancIBD.run
ancIBD.run_ancIBD
ancIBD.run_ancIBDX
ancIBD.transition
N
new_columns() (in module ancIBD.ibd_stats.funcs)
NoPostProcessing (class in ancIBD.postprocessing)
O
opp_homos() (in module ancIBD.IO.h5_load)
(in module ancIBD.plot.plot_opphomos)
output (ancIBD.loaddata.LoadData attribute)
(ancIBD.main.HMM_Full attribute)
(ancIBD.postprocessing.PostProcessing attribute)
(ancIBD.transition.Transitions attribute)
P
p_col (ancIBD.loaddata.LoadH5Multi2 attribute)
(ancIBD.loaddata.LoadHDF5 attribute)
(ancIBD.loaddata.LoadHDF5Multi attribute)
p_model (ancIBD.main.HMM_Full attribute)
path (ancIBD.loaddata.LoadData attribute)
path_h5 (ancIBD.loaddata.LoadH5Multi2 attribute)
(ancIBD.loaddata.LoadHDF5 attribute)
(ancIBD.loaddata.LoadHDF5Multi attribute)
ploidy (ancIBD.loaddata.LoadHDF5Multi attribute)
plot_age_diff() (in module ancIBD.ibd_stats.funcs)
plot_chromosome() (in module ancIBD.plot.plot_karyotype)
plot_gp() (in module ancIBD.IO.h5_qc)
plot_hets() (in module ancIBD.plot.plot_opphomos)
(in module ancIBD.plot.plot_posterior)
plot_identical_gts() (in module ancIBD.plot.plot_opphomos)
plot_karyo_from_ibd_df() (in module ancIBD.plot.plot_karyotype)
plot_opp_homos() (in module ancIBD.plot.plot_opphomos)
plot_pde_individual() (in module ancIBD.plot.plot_karyotype)
plot_pde_individual_from_ibd_df() (in module ancIBD.plot.plot_karyotype)
plot_posterior() (in module ancIBD.plot.plot_posterior)
plot_posterior_IBD2() (in module ancIBD.plot.plot_posterior)
plot_posterior_panel() (in module ancIBD.plot.plot_posterior)
plot_sactter_ibd_target() (in module ancIBD.plot.plot_df)
plot_scatter_ibd() (in module ancIBD.plot.plot_df)
plot_segments_individual() (in module ancIBD.plot.plot_karyotype)
post_model (ancIBD.main.HMM_Full attribute)
PostProcessing (class in ancIBD.postprocessing)
pph_error (ancIBD.loaddata.LoadH5Multi2 attribute)
prep_3x3matrix() (ancIBD.transition.FiveStateTransitions method)
prep_param_list_chrom() (in module ancIBD.run)
prepare_path() (ancIBD.main.HMM_Full method)
print_memory_usage() (in module ancIBD.hmm)
print_runid_missing() (in module ancIBD.IO.batch_run)
R
r_gap (ancIBD.loaddata.LoadSimulated attribute)
r_map (ancIBD.transition.Transitions attribute)
r_path (ancIBD.loaddata.LoadSimulated attribute)
rc_date() (in module ancIBD.ibd_stats.funcs)
remove_iids() (in module ancIBD.ibd_stats.funcs)
reset_print() (ancIBD.main.HMM_Full method)
return_haplotypes_ll() (ancIBD.loaddata.LoadData method)
return_map() (ancIBD.loaddata.LoadData method)
(ancIBD.loaddata.LoadHDF5 method)
return_p() (ancIBD.loaddata.LoadData method)
(ancIBD.loaddata.LoadHDF5 method)
rmap_to_gaps() (ancIBD.transition.FiveStateTransitions method)
roh_posterior() (ancIBD.postprocessing.PostProcessing method)
roh_statistic_df() (in module ancIBD.IO.ind_ibd)
roh_statistics_df() (in module ancIBD.IO.ind_ibd)
run_fwd_bwd() (ancIBD.main.HMM_Full method)
run_fwd_bwd_timed() (ancIBD.main.HMM_Full method)
run_plot_pair() (in module ancIBD.run)
run_plot_pair_IBD2() (in module ancIBD.run)
run_plot_pair_X() (in module ancIBD.run)
S
save (ancIBD.postprocessing.PostProcessing attribute)
save_1240_1000g_kmarkers() (in module ancIBD.IO.prepare_h5)
save_1240kmarkers() (in module ancIBD.IO.prepare_h5)
save_h5() (in module ancIBD.IO.h5_modify)
save_ibd_df() (ancIBD.postprocessing.PostProcessing method)
(in module ancIBD.IO.batch_run)
save_output() (ancIBD.postprocessing.PostProcessing method)
set_params() (ancIBD.emission.Emissions method)
(ancIBD.loaddata.LoadData method)
(ancIBD.main.HMM_Full method)
(ancIBD.postprocessing.PostProcessing method)
(ancIBD.transition.Transitions method)
SevenStateTransitions (class in ancIBD.transition)
submat33 (ancIBD.main.HMM_Full attribute)
T
t_model (ancIBD.main.HMM_Full attribute)
ThreeStateTransitions (class in ancIBD.transition)
to_ibd_df_batches() (in module ancIBD.IO.batch_run)
to_ind_df_batch() (in module ancIBD.IO.batch_run)
to_ind_df_batches() (in module ancIBD.IO.batch_run)
trans_mat (ancIBD.transition.Transitions attribute)
Transitions (class in ancIBD.transition)
TwoStateTransitions (class in ancIBD.transition)
V
vcf_to_1240K_hdf() (in module ancIBD.IO.prepare_h5)
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