Index

A

add_links_to_table() (in module variantcentrifuge.links) 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_snpsift_filter() (in module variantcentrifuge.filters) assign_case_control_counts() (in module variantcentrifuge.helpers)

B

build_sample_phenotype_map() (in module variantcentrifuge.helpers)

C

check_external_tools() (in module variantcentrifuge.utils) check_file() (in module variantcentrifuge.helpers) compute_base_name() (in module variantcentrifuge.pipeline) compute_basic_stats() (in module variantcentrifuge.stats)

compute_gene_stats() (in module variantcentrifuge.stats) compute_impact_summary() (in module variantcentrifuge.stats) compute_variant_type_summary() (in module variantcentrifuge.stats) convert_to_excel() (in module variantcentrifuge.converter)

D

determine_case_control_sets() (in module variantcentrifuge.helpers)

dump_df_to_xlsx() (in module variantcentrifuge.helpers)

E

ensure_fields_in_extract() (in module variantcentrifuge.utils) extract_fields() (in module variantcentrifuge.extractor)

extract_gencode_id() (in module variantcentrifuge.helpers) extract_sample_and_genotype() (in module variantcentrifuge.helpers) extract_variants() (in module variantcentrifuge.filters)

F

filter_dataframe_with_query() (in module variantcentrifuge.filters) filter_final_tsv_by_genotype() (in module variantcentrifuge.filters)

filter_phenotypes() (in module variantcentrifuge.phenotype_filter) filter_tsv_with_expression() (in module variantcentrifuge.filters) finalize_excel_file() (in module variantcentrifuge.converter)

G

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_gene_bed() (in module variantcentrifuge.gene_bed)

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)

L

load_config() (in module variantcentrifuge.config) load_gene_list() (in module variantcentrifuge.helpers)

load_phenotypes() (in module variantcentrifuge.phenotype) load_terms_from_file() (in module variantcentrifuge.pipeline)

M

main() (in module variantcentrifuge.cli) match_IGV_link_columns() (in module variantcentrifuge.helpers) merge_and_format_stats() (in module variantcentrifuge.stats) module variantcentrifuge.analyze_variants 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.phenotype_filter variantcentrifuge.pipeline variantcentrifuge.replacer variantcentrifuge.stats variantcentrifuge.utils variantcentrifuge.validators

N

normalize_genes() (in module variantcentrifuge.gene_bed)

normalize_snpeff_headers() (in module variantcentrifuge.utils) normalize_vcf_headers() (in module variantcentrifuge.utils)

P

parse_bam_mapping() (in module variantcentrifuge.generate_igv_report) parse_samples_from_vcf() (in module variantcentrifuge.pipeline)

perform_gene_burden_analysis() (in module variantcentrifuge.gene_burden) produce_report_json() (in module variantcentrifuge.converter)

R

read_sequencing_manifest() (in module variantcentrifuge.helpers) remove_vcf_extensions() (in module variantcentrifuge.pipeline)

replace_genotypes() (in module variantcentrifuge.replacer) run_command() (in module variantcentrifuge.utils) run_pipeline() (in module variantcentrifuge.pipeline)

S

sanitize_metadata_field() (in module variantcentrifuge.utils)

split_bed_file() (in module variantcentrifuge.utils)

V

validate_igv_files() (in module variantcentrifuge.validators) validate_mandatory_parameters() (in module variantcentrifuge.validators) validate_phenotype_file() (in module variantcentrifuge.validators) validate_vcf_file() (in module variantcentrifuge.validators) variantcentrifuge.analyze_variants 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.phenotype_filter module variantcentrifuge.pipeline module variantcentrifuge.replacer module variantcentrifuge.stats module variantcentrifuge.utils module variantcentrifuge.validators module