Index

A

agg_vars() (bge_toolkit.qc.ConcordanceTable method) ALL_AGG (in module bge_toolkit.qc)

ALL_GROUP (in module bge_toolkit.qc) ancestry_pop (bge_toolkit.qc.SampleQCResult property)

C

calculate_sample_qc_stats() (in module bge_toolkit.qc) chimera_reads (bge_toolkit.qc.SampleQCResult property) close() (bge_toolkit.qc.ConcordanceTable method) (bge_toolkit.qc.JointCallSet method) (bge_toolkit.qc.SampleQCResult method)

compute_pcs() (in module bge_toolkit.qc) concordance() (in module bge_toolkit.qc) concordance_rate (bge_toolkit.qc.Statistic attribute) ConcordanceTable (class in bge_toolkit.qc) ConcordanceView (class in bge_toolkit.qc) contamination (bge_toolkit.qc.SampleQCResult property)

D

dp_bin() (in module bge_toolkit.common)

E

estimate_call_rate_through_gq_stats() (in module bge_toolkit.qc) export() (bge_toolkit.qc.ConcordanceView method) (bge_toolkit.qc.SampleQCResult method)

export_all() (bge_toolkit.qc.ConcordanceView method)

F

f1_score (bge_toolkit.qc.Statistic attribute) fields (bge_toolkit.qc.ConcordanceView attribute) filter_chimeric_reads() (in module bge_toolkit.qc) filter_contamination_rate() (in module bge_toolkit.qc)

filter_genotypes() (in module bge_toolkit.qc) filter_to() (bge_toolkit.qc.SampleQCResult method) filter_to_high_quality_common_sites() (in module bge_toolkit.qc) filter_to_high_quality_exome_intervals() (in module bge_toolkit.qc) full_outer_join() (bge_toolkit.qc.JointCallSet method)

G

get_view() (bge_toolkit.qc.ConcordanceTable method) global_concordance() (bge_toolkit.qc.JointCallSet method)

gq_bin() (in module bge_toolkit.common) gq_fraction (bge_toolkit.qc.SampleQCResult property) group_vars() (bge_toolkit.qc.ConcordanceTable method)

I

identify_outliers_in_qc_stats() (in module bge_toolkit.qc) impute_and_check_sex() (in module bge_toolkit.qc)

infer_ancestry() (in module bge_toolkit.qc) info_score_bin() (in module bge_toolkit.common) inner (bge_toolkit.qc.JoinType attribute)

J

JointCallSet (class in bge_toolkit.qc)

JoinType (class in bge_toolkit.qc)

L

load() (bge_toolkit.qc.ConcordanceTable static method) (bge_toolkit.qc.SampleQCResult static method)

M

mac_bin() (in module bge_toolkit.common)

maf_bin() (in module bge_toolkit.common) max_gp_bin() (in module bge_toolkit.common)

N

n_sample_overlaps (bge_toolkit.qc.JointCallSet property)

n_variant_overlaps (bge_toolkit.qc.JointCallSet property) nonref_concordance_rate (bge_toolkit.qc.Statistic attribute)

O

outer (bge_toolkit.qc.JoinType attribute)

P

passing_samples() (bge_toolkit.qc.SampleQCResult method) pcs (bge_toolkit.qc.SampleQCResult property) plot() (bge_toolkit.qc.ConcordanceView method) plot_all() (bge_toolkit.qc.ConcordanceView method)

plot_chimera_reads() (bge_toolkit.qc.SampleQCResult method) plot_gq_fraction_density() (bge_toolkit.qc.SampleQCResult method) plot_pcs() (bge_toolkit.qc.SampleQCResult method) plot_qc_metric_boxplots() (bge_toolkit.qc.SampleQCResult method) plot_qc_metric_density() (bge_toolkit.qc.SampleQCResult method)

Q

qc_metrics (bge_toolkit.qc.SampleQCResult property)

qual_approx_bin() (in module bge_toolkit.common)

R

result() (bge_toolkit.qc.ConcordanceView method)

S

sample_concordance() (bge_toolkit.qc.JointCallSet method) sample_id (bge_toolkit.qc.SampleQCResult property) sample_overlaps() (bge_toolkit.qc.JointCallSet method) sample_qc() (in module bge_toolkit.qc)

SampleQCResult (class in bge_toolkit.qc) select_high_quality_common_sites() (in module bge_toolkit.qc) sex_info (bge_toolkit.qc.SampleQCResult property) Statistic (class in bge_toolkit.qc)

T

table (bge_toolkit.qc.SampleQCResult property)

V

variant_concordance() (bge_toolkit.qc.JointCallSet method)

variant_overlaps() (bge_toolkit.qc.JointCallSet method)

W

write() (bge_toolkit.qc.ConcordanceTable method) (bge_toolkit.qc.SampleQCResult method)