Index

A

AncestryQC (class in ideal_genom_qc.AncestryQC)

arg_parser() (in module ideal_genom_qc.Helpers)

C

clean_input_folder() (ideal_genom_qc.SampleQC.SampleQC method)

clean_result_folder() (ideal_genom_qc.SampleQC.SampleQC method) compute_pcas() (ideal_genom_qc.UMAPplot.UMAPplot method)

D

delete_temp_files() (in module ideal_genom_qc.Helpers)

draw_pca_plot() (ideal_genom_qc.AncestryQC.GenomicOutlierAnalyzer method)

E

execute_different_genotype_call_rate() (ideal_genom_qc.VariantQC.VariantQC method) execute_drop_ancestry_outliers() (ideal_genom_qc.AncestryQC.GenomicOutlierAnalyzer method) execute_drop_samples() (ideal_genom_qc.SampleQC.SampleQC method) execute_drop_variants() (ideal_genom_qc.VariantQC.VariantQC method) execute_duplicate_relatedness() (ideal_genom_qc.SampleQC.SampleQC method) execute_filter_prob_snps() (ideal_genom_qc.AncestryQC.ReferenceGenomicMerger method) execute_fix_allele_flip() (ideal_genom_qc.AncestryQC.ReferenceGenomicMerger method) execute_fix_chromosome_mismatch() (ideal_genom_qc.AncestryQC.ReferenceGenomicMerger method) execute_fix_possition_mismatch() (ideal_genom_qc.AncestryQC.ReferenceGenomicMerger method) execute_haploid_to_missing() (ideal_genom_qc.SampleQC.SampleQC method) execute_heterozygosity_rate() (ideal_genom_qc.SampleQC.SampleQC method)

execute_hwe_test() (ideal_genom_qc.VariantQC.VariantQC method) execute_ibd() (ideal_genom_qc.SampleQC.SampleQC method) execute_kingship() (ideal_genom_qc.SampleQC.SampleQC method) execute_ld_pruning() (ideal_genom_qc.AncestryQC.ReferenceGenomicMerger method) (ideal_genom_qc.SampleQC.SampleQC method) execute_merge_data() (ideal_genom_qc.AncestryQC.ReferenceGenomicMerger method) execute_miss_genotype() (ideal_genom_qc.SampleQC.SampleQC method) execute_missing_data_rate() (ideal_genom_qc.VariantQC.VariantQC method) execute_pca() (ideal_genom_qc.AncestryQC.GenomicOutlierAnalyzer method) execute_remove_mismatches() (ideal_genom_qc.AncestryQC.ReferenceGenomicMerger method) execute_rename_snpid() (ideal_genom_qc.SampleQC.SampleQC method) execute_sex_check() (ideal_genom_qc.SampleQC.SampleQC method)

F

Fetcher1000Genome (class in ideal_genom_qc.get_references)

FetcherLDRegions (class in ideal_genom_qc.get_references) find_ancestry_outliers() (ideal_genom_qc.AncestryQC.GenomicOutlierAnalyzer method)

G

generate_plots() (ideal_genom_qc.UMAPplot.UMAPplot method) GenomicOutlierAnalyzer (class in ideal_genom_qc.AncestryQC) get_1000genomes() (ideal_genom_qc.get_references.Fetcher1000Genome method)

get_1000genomes_binaries() (ideal_genom_qc.get_references.Fetcher1000Genome method) get_fail_samples() (ideal_genom_qc.SampleQC.SampleQC method) get_fail_variants() (ideal_genom_qc.VariantQC.VariantQC method) get_ld_regions() (ideal_genom_qc.get_references.FetcherLDRegions method)

I

ideal_genom_qc.AncestryQC module ideal_genom_qc.get_references module ideal_genom_qc.Helpers module

ideal_genom_qc.SampleQC module ideal_genom_qc.UMAPplot module ideal_genom_qc.VariantQC module

L

ld_pruning() (ideal_genom_qc.UMAPplot.UMAPplot method)

M

merge_reference_study() (ideal_genom_qc.AncestryQC.AncestryQC method) module ideal_genom_qc.AncestryQC ideal_genom_qc.get_references ideal_genom_qc.Helpers ideal_genom_qc.SampleQC ideal_genom_qc.UMAPplot ideal_genom_qc.VariantQC

R

ReferenceGenomicMerger (class in ideal_genom_qc.AncestryQC) report_call_rate() (ideal_genom_qc.SampleQC.SampleQC method) report_different_genotype_call_rate() (ideal_genom_qc.VariantQC.VariantQC method) report_heterozygosity_rate() (ideal_genom_qc.SampleQC.SampleQC method)

report_hwe() (ideal_genom_qc.VariantQC.VariantQC method) report_ibd_analysis() (ideal_genom_qc.SampleQC.SampleQC method) report_missing_data() (ideal_genom_qc.VariantQC.VariantQC method) report_sex_check() (ideal_genom_qc.SampleQC.SampleQC method) run_pca() (ideal_genom_qc.AncestryQC.AncestryQC method)

S

SampleQC (class in ideal_genom_qc.SampleQC)

shell_do() (in module ideal_genom_qc.Helpers)

U

UMAPplot (class in ideal_genom_qc.UMAPplot)

V

VariantQC (class in ideal_genom_qc.VariantQC)