Index

_

__enter__() (variantcentrifuge.checkpoint.AtomicFileOperation method) (variantcentrifuge.checkpoint.CheckpointContext method) __exit__() (variantcentrifuge.checkpoint.AtomicFileOperation method) (variantcentrifuge.checkpoint.CheckpointContext method) __getstate__() (variantcentrifuge.checkpoint.PipelineState method) __init__() (variantcentrifuge.association.AssociationConfig method) (variantcentrifuge.association.AssociationEngine method) (variantcentrifuge.association.TestResult method) (variantcentrifuge.checkpoint.AtomicFileOperation method) (variantcentrifuge.checkpoint.CheckpointContext method) (variantcentrifuge.checkpoint.FileInfo method) (variantcentrifuge.checkpoint.PipelineState method) (variantcentrifuge.checkpoint.StepInfo method)

__setstate__() (variantcentrifuge.checkpoint.PipelineState method)

A

add_input_file() (variantcentrifuge.checkpoint.CheckpointContext method) add_links_to_table() (in module variantcentrifuge.links) add_output_file() (variantcentrifuge.checkpoint.CheckpointContext method) aggregate_phenotypes_for_samples() (in module variantcentrifuge.phenotype) analyze_variants() (in module variantcentrifuge.analyze_variants) annotate_variants_with_gene_lists() (in module variantcentrifuge.helpers) append_tsv_as_sheet() (in module variantcentrifuge.converter) apply_bcftools_prefilter() (in module variantcentrifuge.filters)

apply_correction() (in module variantcentrifuge.association) apply_snpsift_filter() (in module variantcentrifuge.filters) assign_case_control_counts() (in module variantcentrifuge.helpers) association_workers (variantcentrifuge.association.AssociationConfig attribute) AssociationConfig (class in variantcentrifuge.association) AssociationEngine (class in variantcentrifuge.association) AssociationTest (class in variantcentrifuge.association) AtomicFileOperation (class in variantcentrifuge.checkpoint)

B

build_bcftools_format_string() (in module variantcentrifuge.extractor)

build_pipeline_stages() (in module variantcentrifuge.pipeline) build_sample_phenotype_map() (in module variantcentrifuge.helpers)

C

can_resume() (variantcentrifuge.checkpoint.PipelineState method) can_resume_from_stage() (variantcentrifuge.checkpoint.PipelineState method) categorical_covariates (variantcentrifuge.association.AssociationConfig attribute) check_dependencies() (variantcentrifuge.association.AssociationTest method), [1] check_external_tools() (in module variantcentrifuge.utils) check_file() (in module variantcentrifuge.helpers) check_scoring_requires_inheritance() (in module variantcentrifuge.pipeline) checkpoint() (in module variantcentrifuge.checkpoint) CheckpointContext (class in variantcentrifuge.checkpoint) checksum (variantcentrifuge.checkpoint.FileInfo attribute) ci_lower (variantcentrifuge.association.TestResult attribute) ci_upper (variantcentrifuge.association.TestResult attribute) cleanup_stale_stages() (variantcentrifuge.checkpoint.PipelineState method) clear_step_completion() (variantcentrifuge.checkpoint.PipelineState method) coast_backend (variantcentrifuge.association.AssociationConfig attribute) coast_classification (variantcentrifuge.association.AssociationConfig attribute) coast_weights (variantcentrifuge.association.AssociationConfig attribute) command_hash (variantcentrifuge.checkpoint.StepInfo attribute)

complete_step() (variantcentrifuge.checkpoint.PipelineState method) compute_base_name() (in module variantcentrifuge.utils) compute_basic_stats() (in module variantcentrifuge.stats) compute_custom_stats() (in module variantcentrifuge.stats) compute_gene_stats() (in module variantcentrifuge.stats) compute_impact_summary() (in module variantcentrifuge.stats) compute_phenotype_based_case_control_assignment() (in module variantcentrifuge.helpers) compute_variant_type_summary() (in module variantcentrifuge.stats) confidence_interval_alpha (variantcentrifuge.association.AssociationConfig attribute) confidence_interval_method (variantcentrifuge.association.AssociationConfig attribute) continuity_correction (variantcentrifuge.association.AssociationConfig attribute) convert_to_excel() (in module variantcentrifuge.converter) corrected_p_value (variantcentrifuge.association.TestResult attribute) correction_method (variantcentrifuge.association.AssociationConfig attribute) covariate_columns (variantcentrifuge.association.AssociationConfig attribute) covariate_file (variantcentrifuge.association.AssociationConfig attribute) create_parser() (in module variantcentrifuge.cli) create_stages_from_config() (in module variantcentrifuge.pipeline)

D

determine_case_control_sets() (in module variantcentrifuge.helpers) diagnostics_output (variantcentrifuge.association.AssociationConfig attribute)

dump_df_to_xlsx() (in module variantcentrifuge.helpers) duration (variantcentrifuge.checkpoint.StepInfo property)

E

effect_column_names() (variantcentrifuge.association.AssociationTest method) effect_size (variantcentrifuge.association.TestResult attribute) end_time (variantcentrifuge.checkpoint.StepInfo attribute) ensure_fields_in_extract() (in module variantcentrifuge.utils) error (variantcentrifuge.checkpoint.StepInfo attribute) extra (variantcentrifuge.association.TestResult attribute) extract_fields() (in module variantcentrifuge.extractor)

extract_fields_bcftools() (in module variantcentrifuge.extractor) extract_fields_snpsift() (in module variantcentrifuge.extractor) extract_gencode_id() (in module variantcentrifuge.helpers) extract_phenotypes_for_gt_row() (in module variantcentrifuge.phenotype) extract_phenotypes_from_sample_columns() (in module variantcentrifuge.phenotype) extract_sample_and_genotype() (in module variantcentrifuge.helpers) extract_variants() (in module variantcentrifuge.filters)

F

fail_step() (variantcentrifuge.checkpoint.PipelineState method) FileInfo (class in variantcentrifuge.checkpoint) filter_dataframe_with_query() (in module variantcentrifuge.filters) filter_final_tsv_by_genotype() (in module variantcentrifuge.filters) filter_tsv_with_expression() (in module variantcentrifuge.filters) finalize() (variantcentrifuge.association.AssociationTest method)

finalize_excel_file() (in module variantcentrifuge.converter) finalize_step() (variantcentrifuge.checkpoint.PipelineState method) firth_max_iter (variantcentrifuge.association.AssociationConfig attribute) format_phenotypes_like_gt_column() (in module variantcentrifuge.phenotype) from_dict() (variantcentrifuge.checkpoint.StepInfo class method) from_file() (variantcentrifuge.checkpoint.FileInfo class method) from_names() (variantcentrifuge.association.AssociationEngine class method)

G

gene (variantcentrifuge.association.TestResult attribute) gene_burden_mode (variantcentrifuge.association.AssociationConfig attribute) gene_prior_weight_column (variantcentrifuge.association.AssociationConfig attribute) gene_prior_weights (variantcentrifuge.association.AssociationConfig attribute) generate_html_report() (in module variantcentrifuge.generate_html_report) generate_igv_report() (in module variantcentrifuge.generate_igv_report) generate_igv_safe_filename_base() (in module variantcentrifuge.utils) genotype_to_allele_count() (in module variantcentrifuge.helpers) get_available_resume_points() (variantcentrifuge.checkpoint.PipelineState method) get_completed_stages() (variantcentrifuge.checkpoint.PipelineState method)

get_detailed_status() (variantcentrifuge.checkpoint.PipelineState method) get_gene_bed() (in module variantcentrifuge.gene_bed) get_resume_point() (variantcentrifuge.checkpoint.PipelineState method) get_stages_to_execute() (variantcentrifuge.checkpoint.PipelineState method) get_summary() (variantcentrifuge.checkpoint.PipelineState method) get_tool_version() (in module variantcentrifuge.utils) get_vcf_names() (in module variantcentrifuge.helpers) get_vcf_regions() (in module variantcentrifuge.helpers) get_vcf_samples() (in module variantcentrifuge.helpers) get_vcf_size() (in module variantcentrifuge.helpers)

I

initialize() (variantcentrifuge.checkpoint.PipelineState method)

input_files (variantcentrifuge.checkpoint.StepInfo attribute)

L

load() (variantcentrifuge.checkpoint.PipelineState method) load_config() (in module variantcentrifuge.config)

load_gene_list() (in module variantcentrifuge.helpers) load_phenotypes() (in module variantcentrifuge.phenotype)

M

main() (in module variantcentrifuge.cli) match_igv_link_columns() (in module variantcentrifuge.helpers) max_case_control_ratio (variantcentrifuge.association.AssociationConfig attribute) merge_and_format_stats() (in module variantcentrifuge.stats) min_case_carriers (variantcentrifuge.association.AssociationConfig attribute) min_cases (variantcentrifuge.association.AssociationConfig attribute) missing_sample_threshold (variantcentrifuge.association.AssociationConfig attribute) missing_site_threshold (variantcentrifuge.association.AssociationConfig attribute) module variantcentrifuge.analyze_variants variantcentrifuge.association variantcentrifuge.checkpoint variantcentrifuge.cli variantcentrifuge.config variantcentrifuge.converter variantcentrifuge.extractor variantcentrifuge.filters variantcentrifuge.gene_bed variantcentrifuge.gene_burden variantcentrifuge.generate_html_report variantcentrifuge.generate_igv_report variantcentrifuge.helpers variantcentrifuge.links variantcentrifuge.phenotype variantcentrifuge.pipeline variantcentrifuge.stats variantcentrifuge.utils variantcentrifuge.validators

mtime (variantcentrifuge.checkpoint.FileInfo attribute)

N

n_cases (variantcentrifuge.association.TestResult attribute) n_controls (variantcentrifuge.association.TestResult attribute) n_variants (variantcentrifuge.association.TestResult attribute)

name (variantcentrifuge.association.AssociationTest property) (variantcentrifuge.checkpoint.StepInfo attribute) normalize_genes() (in module variantcentrifuge.gene_bed) normalize_vcf_headers() (in module variantcentrifuge.utils)

O

output_files (variantcentrifuge.checkpoint.StepInfo attribute)

P

p_value (variantcentrifuge.association.TestResult attribute) parameters (variantcentrifuge.checkpoint.StepInfo attribute) parse_ann_subfields() (in module variantcentrifuge.extractor) parse_args() (in module variantcentrifuge.cli) parse_bam_mapping() (in module variantcentrifuge.generate_igv_report) parse_nmd_subfields() (in module variantcentrifuge.extractor) path (variantcentrifuge.checkpoint.FileInfo attribute)

pca_components (variantcentrifuge.association.AssociationConfig attribute) pca_file (variantcentrifuge.association.AssociationConfig attribute) pca_tool (variantcentrifuge.association.AssociationConfig attribute) perform_gene_burden_analysis() (in module variantcentrifuge.gene_burden) PipelineState (class in variantcentrifuge.checkpoint) prepare() (variantcentrifuge.association.AssociationTest method) produce_report_json() (in module variantcentrifuge.converter)

R

read_sequencing_manifest() (in module variantcentrifuge.helpers) remove_vcf_extensions() (in module variantcentrifuge.utils) run() (variantcentrifuge.association.AssociationTest method), [1]

run_all() (variantcentrifuge.association.AssociationEngine method) run_command() (in module variantcentrifuge.utils) run_pipeline() (in module variantcentrifuge.pipeline)

S

sanitize_metadata_field() (in module variantcentrifuge.utils) save() (variantcentrifuge.checkpoint.PipelineState method) se (variantcentrifuge.association.TestResult attribute) should_skip_step() (variantcentrifuge.checkpoint.PipelineState method) size (variantcentrifuge.checkpoint.FileInfo attribute) skat_backend (variantcentrifuge.association.AssociationConfig attribute) skat_method (variantcentrifuge.association.AssociationConfig attribute)

smart_open() (in module variantcentrifuge.utils) split_bed_file() (in module variantcentrifuge.utils) start_step() (variantcentrifuge.checkpoint.PipelineState method) start_time (variantcentrifuge.checkpoint.StepInfo attribute) STATE_FILE_NAME (variantcentrifuge.checkpoint.PipelineState attribute) STATE_VERSION (variantcentrifuge.checkpoint.PipelineState attribute) status (variantcentrifuge.checkpoint.StepInfo attribute) StepInfo (class in variantcentrifuge.checkpoint)

T

test_name (variantcentrifuge.association.TestResult attribute) TestResult (class in variantcentrifuge.association)

to_dict() (variantcentrifuge.checkpoint.StepInfo method) trait_type (variantcentrifuge.association.AssociationConfig attribute)

V

validate() (variantcentrifuge.checkpoint.FileInfo method) validate_igv_files() (in module variantcentrifuge.validators) validate_mandatory_parameters() (in module variantcentrifuge.validators) validate_phenotype_file() (in module variantcentrifuge.validators) validate_resume_from_stage() (variantcentrifuge.checkpoint.PipelineState method) validate_vcf_file() (in module variantcentrifuge.validators) variant_weight_params (variantcentrifuge.association.AssociationConfig attribute) variant_weights (variantcentrifuge.association.AssociationConfig attribute) variantcentrifuge.analyze_variants module variantcentrifuge.association module variantcentrifuge.checkpoint module variantcentrifuge.cli module variantcentrifuge.config module variantcentrifuge.converter module variantcentrifuge.extractor module variantcentrifuge.filters module

variantcentrifuge.gene_bed module variantcentrifuge.gene_burden module variantcentrifuge.generate_html_report module variantcentrifuge.generate_igv_report module variantcentrifuge.helpers module variantcentrifuge.links module variantcentrifuge.phenotype module variantcentrifuge.pipeline module variantcentrifuge.stats module variantcentrifuge.utils module variantcentrifuge.validators module