Index

_

__init__() (ideal_genom.core.get_references.AssemblyReferenceFetcher method) (ideal_genom.core.get_references.Ensembl37Fetcher method) (ideal_genom.core.get_references.Ensembl38Fetcher method) (ideal_genom.core.get_references.Fetcher1000Genome method) (ideal_genom.core.get_references.FetcherLDRegions method) (ideal_genom.core.get_references.ReferenceDataFetcher method) (ideal_genom.core.get_references.RefSeqFetcher method) (ideal_genom.core.pipeline.PipelineExecutor method) (ideal_genom.gwas.gen_linear_mix_model.GWAS_GLMM method) (ideal_genom.gwas.gen_linear_model.GWAS_GLM method) (ideal_genom.gwas.preparatory.Preparatory method) (ideal_genom.population.projection.DimensionalityReductionPipeline method) (ideal_genom.population.projection.PCAReduction method) (ideal_genom.population.projection.Plot2D method) (ideal_genom.population.projection.TSNEReduction method) (ideal_genom.population.projection.UMAPReduction method) (ideal_genom.post_imputation.vcf_process.AnnotateVCF method) (ideal_genom.post_imputation.vcf_process.FilterVariants method) (ideal_genom.post_imputation.vcf_process.IndexVCF method) (ideal_genom.post_imputation.vcf_process.NormalizeVCF method) (ideal_genom.post_imputation.vcf_process.ParallelTaskRunner method) (ideal_genom.post_imputation.vcf_process.ProcessVCF method) (ideal_genom.post_imputation.vcf_process.ReferenceNormalizeVCF method) (ideal_genom.post_imputation.vcf_process.UnzipVCF method) (ideal_genom.post_imputation.vcf_to_plink.GetPLINK method) (ideal_genom.qc.ancestry_qc.AncestryQC method) (ideal_genom.qc.ancestry_qc.AncestryQCReport method) (ideal_genom.qc.sample_qc.SampleQC method) (ideal_genom.qc.sample_qc.SampleQCCleanUp method) (ideal_genom.qc.sample_qc.SampleQCReport method) (ideal_genom.qc.variant_qc.VariantQC method) (ideal_genom.qc.variant_qc.VariantQCCleanUp method) (ideal_genom.qc.variant_qc.VariantQCReport method)

A

AncestryQC (class in ideal_genom.qc.ancestry_qc) AncestryQCReport (class in ideal_genom.qc.ancestry_qc) annotate_snp() (in module ideal_genom.utilities.annotations) annotate_top_hits() (ideal_genom.gwas.gen_linear_mix_model.GWAS_GLMM method) (ideal_genom.gwas.gen_linear_model.GWAS_GLM method)

annotate_variants() (in module ideal_genom.utilities.annotations) annotate_vcf() (ideal_genom.post_imputation.vcf_process.AnnotateVCF method) annotate_with_ensembl() (in module ideal_genom.utilities.annotations) annotate_with_refseq() (in module ideal_genom.utilities.annotations) AnnotateVCF (class in ideal_genom.post_imputation.vcf_process) AssemblyReferenceFetcher (class in ideal_genom.core.get_references)

B

base_output_dir (ideal_genom.core.pipeline.PipelineExecutor attribute) base_url (ideal_genom.core.get_references.Ensembl37Fetcher attribute) (ideal_genom.core.get_references.Ensembl38Fetcher attribute) (ideal_genom.core.get_references.ReferenceDataFetcher attribute) (ideal_genom.core.get_references.RefSeqFetcher attribute) bed_file (ideal_genom.core.get_references.Fetcher1000Genome attribute) beta_beta_plot() built-in function bim_file (ideal_genom.core.get_references.Fetcher1000Genome attribute) build (ideal_genom.core.get_references.Ensembl37Fetcher attribute) (ideal_genom.core.get_references.Ensembl38Fetcher attribute) (ideal_genom.core.get_references.Fetcher1000Genome attribute) (ideal_genom.core.get_references.ReferenceDataFetcher attribute) (ideal_genom.core.get_references.RefSeqFetcher attribute) (ideal_genom.gwas.preparatory.Preparatory attribute) (ideal_genom.post_imputation.vcf_process.ReferenceNormalizeVCF attribute)

built (ideal_genom.core.get_references.FetcherLDRegions attribute) built-in function beta_beta_plot() compute_ld() compute_relative_pos() create_zoom_heatmap() filter_sumstats() manhattan() miami() qqplot_draw() trumpet_plot_binary() trumpet_plot_quantitative()

C

clean_all() (ideal_genom.qc.sample_qc.SampleQCCleanUp method) (ideal_genom.qc.variant_qc.VariantQCCleanUp method) clean_dir (ideal_genom.qc.sample_qc.SampleQC attribute) clean_input_files() (ideal_genom.qc.sample_qc.SampleQCCleanUp method) clean_results_files() (ideal_genom.qc.sample_qc.SampleQCCleanUp method) cmd_run() (in module ideal_genom.core.cli) cmd_template() (in module ideal_genom.core.cli) cmd_validate() (in module ideal_genom.core.cli) CommandExecutionError compute_grm() (ideal_genom.gwas.gen_linear_mix_model.GWAS_GLMM method)

compute_ld() built-in function compute_relative_pos() built-in function config (ideal_genom.core.pipeline.PipelineExecutor attribute) ConfigurationError convert_vcf_to_plink() (ideal_genom.post_imputation.vcf_to_plink.GetPLINK method) count_file_lines() (in module ideal_genom.core.utils) create_parser() (in module ideal_genom.core.cli) create_zoom_heatmap() built-in function

D

destination (ideal_genom.core.get_references.Fetcher1000Genome attribute) (ideal_genom.core.get_references.FetcherLDRegions attribute) destination_folder (ideal_genom.core.get_references.Ensembl38Fetcher attribute) (ideal_genom.core.get_references.ReferenceDataFetcher attribute)

DimensionalityReductionPipeline (class in ideal_genom.population.projection) download_file() (in module ideal_genom.core.utils) download_latest() (ideal_genom.core.get_references.ReferenceDataFetcher method) download_reference_file() (ideal_genom.core.get_references.AssemblyReferenceFetcher method) draw_pca_plot() (ideal_genom.qc.ancestry_qc.AncestryQCReport method)

E

Ensembl37Fetcher (class in ideal_genom.core.get_references) Ensembl38Fetcher (class in ideal_genom.core.get_references) excute_intermediate_cleanup() (ideal_genom.post_imputation.vcf_process.ProcessVCF method) execute() (ideal_genom.core.pipeline.PipelineExecutor method) execute_ancestry_qc_pipeline() (ideal_genom.qc.ancestry_qc.AncestryQC method) execute_annotate() (ideal_genom.post_imputation.vcf_process.ProcessVCF method) execute_concatenate() (ideal_genom.post_imputation.vcf_process.ProcessVCF method) execute_different_genotype_call_rate() (ideal_genom.qc.variant_qc.VariantQC method) execute_dimensionality_reduction_pipeline() (ideal_genom.population.projection.DimensionalityReductionPipeline method) execute_drop_samples() (ideal_genom.qc.sample_qc.SampleQC method) execute_drop_variants() (ideal_genom.qc.variant_qc.VariantQC method) execute_duplicate_relatedness() (ideal_genom.qc.sample_qc.SampleQC method) execute_filter() (ideal_genom.post_imputation.vcf_process.ProcessVCF method) execute_gwas_glm_pipeline() (ideal_genom.gwas.gen_linear_model.GWAS_GLM method) execute_gwas_glmm_pipeline() (ideal_genom.gwas.gen_linear_mix_model.GWAS_GLMM method) execute_heterozygosity_rate() (ideal_genom.qc.sample_qc.SampleQC method) execute_ibd() (ideal_genom.qc.sample_qc.SampleQC method) execute_index() (ideal_genom.post_imputation.vcf_process.ProcessVCF method) execute_intermediate_cleanup() (ideal_genom.post_imputation.vcf_to_plink.GetPLINK method) execute_kinship() (ideal_genom.qc.sample_qc.SampleQC method) execute_ld_pruning() (ideal_genom.population.projection.PCAReduction method) (ideal_genom.qc.sample_qc.SampleQC method) execute_ld_prunning() (ideal_genom.gwas.preparatory.Preparatory method) execute_miss_genotype() (ideal_genom.qc.sample_qc.SampleQC method) execute_missing_data_rate() (ideal_genom.qc.variant_qc.VariantQC method) execute_normalize() (ideal_genom.post_imputation.vcf_process.ProcessVCF method)

execute_parameter_grid() (ideal_genom.population.projection.DimensionalityReductionPipeline method) execute_pc_decomposition() (ideal_genom.gwas.preparatory.Preparatory method) execute_pca() (ideal_genom.population.projection.PCAReduction method) (ideal_genom.qc.ancestry_qc.AncestryQC method) execute_pca_preparation() (ideal_genom.population.projection.DimensionalityReductionPipeline method) execute_pcareduction_pipeline() (ideal_genom.population.projection.PCAReduction method) execute_plink_conversion_pipeline() (ideal_genom.post_imputation.vcf_to_plink.GetPLINK method) execute_preparatory_pipeline() (ideal_genom.gwas.preparatory.Preparatory method) execute_preprocessing() (ideal_genom.qc.sample_qc.SampleQC method) execute_process_vcf_pipeline() (ideal_genom.post_imputation.vcf_process.ProcessVCF method) execute_reference_normalize() (ideal_genom.post_imputation.vcf_process.ProcessVCF method) execute_rename_snpid() (ideal_genom.post_imputation.vcf_to_plink.GetPLINK method) execute_sample_qc_pipeline() (ideal_genom.qc.sample_qc.SampleQC method) execute_sex_check() (ideal_genom.qc.sample_qc.SampleQC method) execute_task() (ideal_genom.post_imputation.vcf_process.AnnotateVCF method) (ideal_genom.post_imputation.vcf_process.FilterVariants method) (ideal_genom.post_imputation.vcf_process.IndexVCF method) (ideal_genom.post_imputation.vcf_process.NormalizeVCF method) (ideal_genom.post_imputation.vcf_process.ParallelTaskRunner method) (ideal_genom.post_imputation.vcf_process.ReferenceNormalizeVCF method) (ideal_genom.post_imputation.vcf_process.UnzipVCF method) execute_tsne() (ideal_genom.population.projection.DimensionalityReductionPipeline method) execute_umap() (ideal_genom.population.projection.DimensionalityReductionPipeline method) execute_unzip() (ideal_genom.post_imputation.vcf_process.ProcessVCF method) execute_variant_qc_pipeline() (ideal_genom.qc.variant_qc.VariantQC method) extract_gz_file() (in module ideal_genom.core.utils)

F

fails_dir (ideal_genom.qc.sample_qc.SampleQC attribute) fam_file (ideal_genom.core.get_references.Fetcher1000Genome attribute) Fetcher1000Genome (class in ideal_genom.core.get_references) FetcherLDRegions (class in ideal_genom.core.get_references) file_path (ideal_genom.core.get_references.AssemblyReferenceFetcher attribute) files (ideal_genom.post_imputation.vcf_process.ParallelTaskRunner attribute)

filter_sumstats() built-in function filter_variants() (ideal_genom.post_imputation.vcf_process.FilterVariants method) FilterVariants (class in ideal_genom.post_imputation.vcf_process) fit_transform() (ideal_genom.population.projection.TSNEReduction method) (ideal_genom.population.projection.UMAPReduction method) format_memory_size() (in module ideal_genom.core.utils)

G

generate_plot() (ideal_genom.population.projection.Plot2D method) generate_plots() (ideal_genom.population.projection.DimensionalityReductionPipeline method) get_1000genomes() (ideal_genom.core.get_references.Fetcher1000Genome method) get_1000genomes_binaries() (ideal_genom.core.get_references.Fetcher1000Genome method) get_all_genes() (ideal_genom.core.get_references.ReferenceDataFetcher method) get_available_memory() (in module ideal_genom.core.utils) get_chr_to_NC() (in module ideal_genom.utilities.annotations) get_closest_gene() (in module ideal_genom.utilities.annotations) get_destination_folder() (ideal_genom.core.get_references.ReferenceDataFetcher method) get_fail_samples() (ideal_genom.qc.sample_qc.SampleQC method) get_fail_variants() (ideal_genom.qc.variant_qc.VariantQC method) get_latest_release() (ideal_genom.core.get_references.Ensembl37Fetcher method) (ideal_genom.core.get_references.Ensembl38Fetcher method) (ideal_genom.core.get_references.ReferenceDataFetcher method) (ideal_genom.core.get_references.RefSeqFetcher method)

get_ld_regions() (ideal_genom.core.get_references.FetcherLDRegions method) get_number_to_chr() (in module ideal_genom.utilities.annotations) get_optimal_threads() (in module ideal_genom.core.utils) get_pipeline_summary() (ideal_genom.core.pipeline.PipelineExecutor method) get_reference_url() (ideal_genom.core.get_references.AssemblyReferenceFetcher method) get_step_output() (ideal_genom.core.pipeline.PipelineExecutor method) get_system_resource_info() (in module ideal_genom.core.utils) get_top_hits() (ideal_genom.gwas.gen_linear_mix_model.GWAS_GLMM method) (ideal_genom.gwas.gen_linear_model.GWAS_GLM method) GetPLINK (class in ideal_genom.post_imputation.vcf_to_plink) glm_association_analysis() (ideal_genom.gwas.gen_linear_model.GWAS_GLM method) gtf_file (ideal_genom.core.get_references.ReferenceDataFetcher attribute) gtf_to_all_genes() (in module ideal_genom.utilities.annotations) GWAS_GLM (class in ideal_genom.gwas.gen_linear_model) GWAS_GLMM (class in ideal_genom.gwas.gen_linear_mix_model) gz_file (ideal_genom.core.get_references.ReferenceDataFetcher attribute)

H

hh_to_missing (ideal_genom.qc.sample_qc.SampleQC attribute)

high_ld_file (ideal_genom.gwas.preparatory.Preparatory attribute)

I

ideal_genom.core.cli module ideal_genom.core.config module ideal_genom.core.executor module ideal_genom.core.get_references module ideal_genom.core.pipeline module ideal_genom.core.utils module ideal_genom.gwas.gen_linear_mix_model module ideal_genom.gwas.gen_linear_model module ideal_genom.gwas.preparatory module

ideal_genom.population.projection module ideal_genom.post_imputation.vcf_process module ideal_genom.post_imputation.vcf_to_plink module ideal_genom.utilities.annotations module index_vcf() (ideal_genom.post_imputation.vcf_process.IndexVCF method) IndexVCF (class in ideal_genom.post_imputation.vcf_process) input_name (ideal_genom.gwas.gen_linear_model.GWAS_GLM attribute) (ideal_genom.gwas.preparatory.Preparatory attribute) (ideal_genom.post_imputation.vcf_to_plink.GetPLINK attribute) input_path (ideal_genom.gwas.gen_linear_model.GWAS_GLM attribute) (ideal_genom.gwas.preparatory.Preparatory attribute) (ideal_genom.post_imputation.vcf_process.ParallelTaskRunner attribute) (ideal_genom.post_imputation.vcf_process.ProcessVCF attribute) (ideal_genom.post_imputation.vcf_to_plink.GetPLINK attribute)

L

latest_url (ideal_genom.core.get_references.Ensembl37Fetcher attribute) (ideal_genom.core.get_references.Ensembl38Fetcher attribute) (ideal_genom.core.get_references.ReferenceDataFetcher attribute) (ideal_genom.core.get_references.RefSeqFetcher attribute)

ld_regions (ideal_genom.core.get_references.FetcherLDRegions attribute) load_config() (in module ideal_genom.core.config)

M

main() (in module ideal_genom.core.cli) manhattan() built-in function max_workers (ideal_genom.post_imputation.vcf_process.ParallelTaskRunner attribute) merge_reference_study() (ideal_genom.qc.ancestry_qc.AncestryQC method) miami() built-in function module ideal_genom.core.cli ideal_genom.core.config ideal_genom.core.executor ideal_genom.core.get_references ideal_genom.core.pipeline ideal_genom.core.utils ideal_genom.gwas.gen_linear_mix_model ideal_genom.gwas.gen_linear_model ideal_genom.gwas.preparatory ideal_genom.population.projection ideal_genom.post_imputation.vcf_process ideal_genom.post_imputation.vcf_to_plink ideal_genom.utilities.annotations

N

normalize_vcf() (ideal_genom.post_imputation.vcf_process.NormalizeVCF method)

normalize_with_reference() (ideal_genom.post_imputation.vcf_process.ReferenceNormalizeVCF method) NormalizeVCF (class in ideal_genom.post_imputation.vcf_process)

O

output_name (ideal_genom.gwas.gen_linear_model.GWAS_GLM attribute) (ideal_genom.gwas.preparatory.Preparatory attribute) (ideal_genom.post_imputation.vcf_to_plink.GetPLINK attribute) output_path (ideal_genom.gwas.gen_linear_model.GWAS_GLM attribute) (ideal_genom.gwas.preparatory.Preparatory attribute) (ideal_genom.post_imputation.vcf_process.ParallelTaskRunner attribute) (ideal_genom.post_imputation.vcf_process.ProcessVCF attribute) (ideal_genom.post_imputation.vcf_to_plink.GetPLINK attribute)

output_prefix (ideal_genom.post_imputation.vcf_process.AnnotateVCF attribute) (ideal_genom.post_imputation.vcf_process.FilterVariants attribute) (ideal_genom.post_imputation.vcf_process.ReferenceNormalizeVCF attribute)

P

ParallelTaskRunner (class in ideal_genom.post_imputation.vcf_process) pattern (ideal_genom.post_imputation.vcf_process.IndexVCF attribute) PCAReduction (class in ideal_genom.population.projection) pgen_file (ideal_genom.core.get_references.Fetcher1000Genome attribute) PipelineExecutor (class in ideal_genom.core.pipeline) Plot2D (class in ideal_genom.population.projection) Plot3D (class in ideal_genom.population.projection) plots_dir (ideal_genom.qc.sample_qc.SampleQC attribute)

Preparatory (class in ideal_genom.gwas.preparatory) prepare_aux_files() (ideal_genom.gwas.gen_linear_mix_model.GWAS_GLMM method) prepare_genome() (in module ideal_genom.utilities.annotations) prepare_gtf_path() (in module ideal_genom.utilities.annotations) prepare_metadata() (ideal_genom.population.projection.Plot2D method) ProcessVCF (class in ideal_genom.post_imputation.vcf_process) pruned_file (ideal_genom.qc.sample_qc.SampleQC attribute) psam_file (ideal_genom.core.get_references.Fetcher1000Genome attribute) pvar_file (ideal_genom.core.get_references.Fetcher1000Genome attribute)

Q

qqplot_draw() built-in function

R

r2_threshold (ideal_genom.post_imputation.vcf_process.FilterVariants attribute) recompute (ideal_genom.gwas.gen_linear_model.GWAS_GLM attribute) ref_annotation (ideal_genom.post_imputation.vcf_process.AnnotateVCF attribute) reference_file (ideal_genom.core.get_references.AssemblyReferenceFetcher attribute) (ideal_genom.post_imputation.vcf_process.ReferenceNormalizeVCF attribute) reference_url (ideal_genom.core.get_references.AssemblyReferenceFetcher attribute) ReferenceDataFetcher (class in ideal_genom.core.get_references) ReferenceNormalizeVCF (class in ideal_genom.post_imputation.vcf_process) RefSeqFetcher (class in ideal_genom.core.get_references) renamed_snps (ideal_genom.qc.sample_qc.SampleQC attribute) report_ancestry_qc() (ideal_genom.qc.ancestry_qc.AncestryQCReport method) report_call_rate() (ideal_genom.qc.sample_qc.SampleQCReport method) report_different_genotype_call_rate() (ideal_genom.qc.variant_qc.VariantQC method)

report_heterozygosity_rate() (ideal_genom.qc.sample_qc.SampleQCReport method) report_ibd_analysis() (ideal_genom.qc.sample_qc.SampleQCReport method) report_missing_data() (ideal_genom.qc.variant_qc.VariantQC method) report_pca() (ideal_genom.qc.ancestry_qc.AncestryQCReport method) report_sample_qc() (ideal_genom.qc.sample_qc.SampleQCReport method) report_sex_check() (ideal_genom.qc.sample_qc.SampleQCReport method) report_variant_qc() (ideal_genom.qc.variant_qc.VariantQCReport method) results_dir (ideal_genom.gwas.gen_linear_model.GWAS_GLM attribute) (ideal_genom.qc.sample_qc.SampleQC attribute) run_bcftools() (in module ideal_genom.core.executor) run_gcta() (in module ideal_genom.core.executor) run_gwas_glmm() (ideal_genom.gwas.gen_linear_mix_model.GWAS_GLMM method) run_plink() (in module ideal_genom.core.executor) run_plink2() (in module ideal_genom.core.executor)

S

SampleQC (class in ideal_genom.qc.sample_qc) SampleQCCleanUp (class in ideal_genom.qc.sample_qc) SampleQCReport (class in ideal_genom.qc.sample_qc) setup_logging() (in module ideal_genom.core.cli) shell_do() (in module ideal_genom.core.executor)

source (ideal_genom.core.get_references.Ensembl37Fetcher attribute) (ideal_genom.core.get_references.Ensembl38Fetcher attribute) (ideal_genom.core.get_references.ReferenceDataFetcher attribute) (ideal_genom.core.get_references.RefSeqFetcher attribute) steps (ideal_genom.core.pipeline.PipelineExecutor attribute)

T

trumpet_plot_binary() built-in function

trumpet_plot_quantitative() built-in function TSNEReduction (class in ideal_genom.population.projection)

U

UMAPReduction (class in ideal_genom.population.projection) unzip_file_flat() (in module ideal_genom.core.utils) unzip_files() (ideal_genom.post_imputation.vcf_process.UnzipVCF method)

unzip_latest() (ideal_genom.core.get_references.ReferenceDataFetcher method) unzip_reference_file() (ideal_genom.core.get_references.AssemblyReferenceFetcher method) UnzipVCF (class in ideal_genom.post_imputation.vcf_process) update_fam() (ideal_genom.post_imputation.vcf_to_plink.GetPLINK method)

V

validate_config() (in module ideal_genom.core.config) validate_config_file() (in module ideal_genom.core.cli) validate_file_path() (in module ideal_genom.core.utils) validate_input_file() (in module ideal_genom.core.utils)

validate_output_dir() (in module ideal_genom.core.utils) validate_step() (in module ideal_genom.core.config) VariantQC (class in ideal_genom.qc.variant_qc) VariantQCCleanUp (class in ideal_genom.qc.variant_qc) VariantQCReport (class in ideal_genom.qc.variant_qc)