Welcome to querynator’s documentation!

Contents:

• querynator
  • Features
  • Credits
• Installation
  • Stable release
  • From sources
• Usage
  • VCF Normalization
  • Query the cancergenomeinterpeter - CGI
  • Query the Clinical Interpretations of Variants in Cancer - CIViC
  • Filtering benign variants
  • Create an HTML Report
• API Reference
  • query_api_civic()
  • query_api_cgi()
  • create_report()
  • Cancer()
  • EnumType
  • filter_vcf_by_vep()
  • get_unique_querynator_dir()
  • make_enum()
  • write_vcf()
  • add_cgi_metadata()
  • delete_job_cgi()
  • download_cgi()
  • hg_assembly()
  • query_cgi()
  • status_done()
  • submit_query_cgi()
  • access_civic_by_coordinate()
  • add_civic_metadata()
  • append_to_dict()
  • check_vcf_input()
  • concat_dicts()
  • create_civic_results()
  • get_assertion_information_from_variant()
  • get_coordinates_from_vcf()
  • get_evidence_information_from_variant()
  • get_gene_information_from_variant()
  • get_molecular_profile_information_from_variant()
  • get_positional_information_from_coord_obj()
  • get_querynator_id()
  • get_variant_information_from_variant()
  • query_civic()
  • smoothen_dict()
  • sort_coord_list()
  • sort_rules()
  • vcf_file()
  • add_variant_name_report()
  • assign_comb_evidence_labels()
  • check_if_nan()
  • create_barplot()
  • create_evidence_table()
  • create_html_link()
  • create_link_col()
  • create_report_htmls()
  • create_therapy_table()
  • create_tier_table()
  • create_upsetplots()
  • encode_upsetplot()
  • get_KB_count()
  • get_disease_names_CIViC()
  • get_evidence_description()
  • get_reference_build()
  • get_sources()
  • get_therapy_information_CGI()
  • get_therapy_names()
  • remove_dups()
  • retrieve_info_from_row()
  • save_plot()
  • split_cols()
  • write_individual_report()
  • write_overall_report()
  • combine_cgi()
  • extract_coords()
  • get_all_alterations()
  • get_highest_evidence()
  • link_biomarkers()
  • merge_alterations_vep()
  • read_filtered_vcf()
  • read_modify_alterations()
  • remove_prefix()
  • subset_alterations()
  • combine_civic()
  • merge_civic_vep()
  • read_civic_results()
  • read_filtered_vcf()
  • combine_cgi_civic()
  • merge_civic_cgi()
  • add_tiers_and_scores_to_df()
  • check_nan_in_pair()
  • extract_num()
  • generate_allele_freq_score()
  • generate_consequence_score()
  • generate_evidence_score()
  • generate_pathogenicity_score_score()
  • get_allele_freq_tiering()
  • get_cgi_consequence_score()
  • get_civic_consequence_score()
  • get_consequence_score()
  • get_largest_af()
  • get_largest_path_score()
  • get_min()
  • scoring_variants()
  • subset_variants_into_tiers()
• Contributing
  • Types of Contributions
  • Get Started!
  • Pull Request Guidelines
  • Deploying
• Changelog
  • 0.4.1 - Stormy Saturn (2023-06-13)
  • 0.4.0 - Stormy Saturn (2023-05-31)
  • 0.3.3 - Iron Mercury (2023-05-05)
  • 0.3.2 - Iron Mercury (2023-05-05)
  • 0.3.1 - Iron Mercury (2023-05-05)
  • 0.3.0 - Iron Mercury (2023-05-04)
  • 0.2.2 - Sour Venus (2023-03-16)
  • 0.2.1 - Sour Venus (2023-02-16)
  • 0.2.0 - Sour Venus (2023-02-07)
  • 0.1.3 - Diamond Neptune (2022-11-21)
  • 0.1.2 - Diamond Neptune (2022-11-18)
  • 0.1.1 - Methane Titan (2022-11-18)
  • 0.1.0 - initial release (2022-11-18)

Indices and tables

• Index

• Module Index

• Search Page