# Emedgene Analyze manual - [Getting around the platform](/emedgene-analyze-manual/getting_around_the_platform.md) - [Top navigation panel](/emedgene-analyze-manual/getting_around_the_platform/top_navigation_panel.md) - [Emedgene applications menu](/emedgene-analyze-manual/getting_around_the_platform/emedgene_applications_menu.md) - [Dashboard tab](/emedgene-analyze-manual/getting_around_the_platform/dashboard.md) - [Cases tab](/emedgene-analyze-manual/getting_around_the_platform/cases_tab.md) - [Cases table](/emedgene-analyze-manual/getting_around_the_platform/cases_tab/cases_table.md) - [Cases table navigation panel](/emedgene-analyze-manual/getting_around_the_platform/cases_tab/cases-table-navigation-panel.md) - [Case details](/emedgene-analyze-manual/getting_around_the_platform/cases_tab/case_details.md) - [Case info](/emedgene-analyze-manual/getting_around_the_platform/cases_tab/case_details/case-info.md) - [Family tree](/emedgene-analyze-manual/getting_around_the_platform/cases_tab/case_details/family-tree.md) - [Activity](/emedgene-analyze-manual/getting_around_the_platform/cases_tab/case_details/activity.md) - [How to open a case](/emedgene-analyze-manual/getting_around_the_platform/cases_tab/how-to-open-a-case.md) - [How to customize Cases table view](/emedgene-analyze-manual/getting_around_the_platform/cases_tab/how-to-customize-cases-table-view.md) - [How to filter cases](/emedgene-analyze-manual/getting_around_the_platform/cases_tab/how-to-filter-cases.md) - [How to search for cases](/emedgene-analyze-manual/getting_around_the_platform/cases_tab/browse_and_select_cases.md) - [How to group cases](/emedgene-analyze-manual/getting_around_the_platform/cases_tab/how-to-group-cases.md) - [How to sort cases](/emedgene-analyze-manual/getting_around_the_platform/cases_tab/how-to-sort-cases.md) - [How to delete cases](/emedgene-analyze-manual/getting_around_the_platform/cases_tab/how-to-delete-cases.md) - [Help](/emedgene-analyze-manual/getting_around_the_platform/help.md) - [Okta identity management](/emedgene-analyze-manual/getting_around_the_platform/okta_identity_management.md) - [Managing data storage](/emedgene-analyze-manual/managing_data_storage.md) - [Manage data storages](/emedgene-analyze-manual/managing_data_storage/manage_data_storages.md) - [Manage S3 credentials](/emedgene-analyze-manual/managing_data_storage/manage_s3_credentials.md) - [Manage ICA storage](/emedgene-analyze-manual/managing_data_storage/manage-ica-storage.md) - [Storage providers](/emedgene-analyze-manual/managing_data_storage/storage-providers.md) - [Manage Azure Blob storage](/emedgene-analyze-manual/managing_data_storage/storage-providers/manage_azure_blob_data_storage.md) - [Manage Google Cloud storage](/emedgene-analyze-manual/managing_data_storage/storage-providers/manage-gcs-storage-v37.0+.md) - [Manage BaseSpace storage](/emedgene-analyze-manual/managing_data_storage/storage-providers/manage-basespace-storage.md) - [Bring Your Own Bucket](/emedgene-analyze-manual/managing_data_storage/bring-your-own-bucket.md) - [Bring Your Own Key](/emedgene-analyze-manual/managing_data_storage/bring-your-own-key.md) - [Launching analysis](/emedgene-analyze-manual/launching-analysis.md) - [Creating a single case](/emedgene-analyze-manual/launching-analysis/creating_a_single_case.md) - [Select sample type](/emedgene-analyze-manual/launching-analysis/creating_a_single_case/select_sample_type.md) - [Create a family tree](/emedgene-analyze-manual/launching-analysis/creating_a_single_case/create_a_family_tree.md) - [Family tree legend](/emedgene-analyze-manual/launching-analysis/creating_a_single_case/family_tree_legend.md) - [Add a sample](/emedgene-analyze-manual/launching-analysis/creating_a_single_case/add_a_sample.md) - [Adding patient info for the proband](/emedgene-analyze-manual/launching-analysis/creating_a_single_case/adding_patient_info_for_the_proband.md) - [Adding patient info for the non-proband samples](/emedgene-analyze-manual/launching-analysis/creating_a_single_case/adding_patient_info_for_the_non-proband_samples.md) - [Incidental (secondary) findings](/emedgene-analyze-manual/launching-analysis/creating_a_single_case/secondary_findings.md) - [Case type and region of interest](/emedgene-analyze-manual/launching-analysis/creating_a_single_case/case-type-and-region-of-interest.md) - [Default region of interest kits](/emedgene-analyze-manual/launching-analysis/creating_a_single_case/case-type-and-region-of-interest/genomic_regions_by_case_type.md) - [Sequencing information](/emedgene-analyze-manual/launching-analysis/creating_a_single_case/sequencing-information.md) - [Gene list](/emedgene-analyze-manual/launching-analysis/creating_a_single_case/gene_list.md) - [Preset group](/emedgene-analyze-manual/launching-analysis/creating_a_single_case/preset_groups.md) - [Supported parental ethnicities](/emedgene-analyze-manual/launching-analysis/creating_a_single_case/supported_parental_ethnicities.md) - [Labeling a case](/emedgene-analyze-manual/launching-analysis/creating_a_single_case/labeling_a_case.md) - [Creating multiple cases](/emedgene-analyze-manual/launching-analysis/creating_multiple_cases.md) - [Batch case upload from platform](/emedgene-analyze-manual/launching-analysis/creating_multiple_cases/batch_case_upload.md) - [CSV format requirements](/emedgene-analyze-manual/launching-analysis/creating_multiple_cases/csv_format_requirements.md) - [Batch case upload via CLI](/emedgene-analyze-manual/launching-analysis/creating_multiple_cases/batch-case-upload-via-cli.md) - [Supported variant callers](/emedgene-analyze-manual/supported-vcfs-variant-callers.md) - [Tertiary analysis pipeline](/emedgene-analyze-manual/tertiary-analysis-pipeline.md) - [Supported reference genome assemblies](/emedgene-analyze-manual/tertiary-analysis-pipeline/which_reference_genomes_can_i_use.md) - [Joint calling in Emedgene](/emedgene-analyze-manual/tertiary-analysis-pipeline/how_does_joint_calling_work_on_emedgene.md) - [Transcript prioritization logic](/emedgene-analyze-manual/tertiary-analysis-pipeline/how_does_emedgene_analyze_prioritize_transcripts.md) - [Emedgene annotations and update frequency](/emedgene-analyze-manual/tertiary-analysis-pipeline/annotation_updates.md) - [Variant effect and severity calculation](/emedgene-analyze-manual/tertiary-analysis-pipeline/how_does_emedgene_calculate_variant_effect_and_severity.md) - [Integrating variant annotations from multiple sources](/emedgene-analyze-manual/tertiary-analysis-pipeline/how-does-emedgene-analyze-merge-variants-from-different-sources.md) - [Processing multi-nucleotide variants](/emedgene-analyze-manual/tertiary-analysis-pipeline/how_are_mnvs_handled_on_the_platform.md) - [Annotations from organization databases](/emedgene-analyze-manual/tertiary-analysis-pipeline/annotations-from-organization-databases.md) - [Reviewing a case](/emedgene-analyze-manual/reviewing_a_case.md) - [Individual case page](/emedgene-analyze-manual/reviewing_a_case/individual_case_page.md) - [Case status](/emedgene-analyze-manual/reviewing_a_case/case_status.md) - [Case statuses in a case lifecycle](/emedgene-analyze-manual/reviewing_a_case/case_status/case-statuses-in-a-case-lifecycle.md) - [How to update a case status](/emedgene-analyze-manual/reviewing_a_case/case_status/how-to-update-a-case-status.md) - [Individual case page: Top bar](/emedgene-analyze-manual/reviewing_a_case/individual-case-page-top-bar.md) - [Candidates tab](/emedgene-analyze-manual/reviewing_a_case/candidates-tab.md) - [Reviewing the Candidates tab](/emedgene-analyze-manual/reviewing_a_case/candidates-tab/reviewing-the-candidates-tab.md) - [Most Likely Candidates and Candidates](/emedgene-analyze-manual/reviewing_a_case/candidates-tab/most_likely_candidates_and_candidates.md) - [Lab tab](/emedgene-analyze-manual/reviewing_a_case/lab_tab.md) - [Summary dashboard](/emedgene-analyze-manual/reviewing_a_case/lab_tab/summary-dashboard.md) - [Sequencing lab information section](/emedgene-analyze-manual/reviewing_a_case/lab_tab/sequencing-lab-information-section.md) - [Case quality section](/emedgene-analyze-manual/reviewing_a_case/lab_tab/case-quality-section.md) - [Sample quality section](/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section.md) - [NGS sample quality metrics](/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/ngs-sample-quality-metrics.md) - [NGS sample quality](/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/ngs-sample-quality-metrics/ngs-sample-quality.md) - [NGS sex validation](/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/ngs-sample-quality-metrics/ngs-sex-validation.md) - [Ploidy](/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/ngs-sample-quality-metrics/ploidy.md) - [Contamination](/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/ngs-sample-quality-metrics/contamination.md) - [Coverage](/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/ngs-sample-quality-metrics/coverage.md) - [Percentage of mapped reads](/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/ngs-sample-quality-metrics/percentage-of-mapped-reads.md) - [Sequencing error rate](/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/ngs-sample-quality-metrics/sequencing-error-rate.md) - [Array sample quality metrics](/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/array-sample-quality-metrics.md) - [Array sample quality](/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/array-sample-quality-metrics/array-sample-quality.md) - [Array sex validation](/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/array-sample-quality-metrics/array-sex-validation.md) - [Autosomal call rate](/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/array-sample-quality-metrics/autosomal-call-rate.md) - [Call rate](/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/array-sample-quality-metrics/call-rate.md) - [Log R deviation](/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/array-sample-quality-metrics/log-r-deviation.md) - [DRAGEN QC report](/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/dragen-qc-report.md) - [Prerequisites for accessing the DRAGEN QC report](/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/dragen-qc-report/prerequisites-for-accessing-the-dragen-qc-report.md) - [Prepare DRAGEN QC metrics files to be included in a NGS VCF case](/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/dragen-qc-report/prerequisites-for-accessing-the-dragen-qc-report/how-to-i-prepare-metrics-files-generated-by-dragen-to-be-used-as-input-for-emedgene.md) - [Review interactive DRAGEN report](/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/dragen-qc-report/review-interactive-dragen-report.md) - [Download DRAGEN QC metrics files](/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/dragen-qc-report/download-dragen-qc-metrics-files.md) - [Pedigree section](/emedgene-analyze-manual/reviewing_a_case/lab_tab/pedigree-section.md) - [Genes coverage section](/emedgene-analyze-manual/reviewing_a_case/lab_tab/genes-coverage-section.md) - [Genome view tab](/emedgene-analyze-manual/reviewing_a_case/genome-overview.md) - [Analysis tools tab](/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab.md) - [Analysis tools tab (≤38.0)](/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab/analysis_tools_tab.md) - [Variant table](/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab/analysis_tools_tab/variant_table.md) - [Variant table columns](/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab/analysis_tools_tab/variant_table/variant_table_columns.md) - [Variant table row formatting](/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab/analysis_tools_tab/variant_table/variant-table-row-formatting.md) - [Variant table view customization](/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab/analysis_tools_tab/variant_table/variant-table-view-customization.md) - [Multi-selection of variants and bulk actions](/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab/analysis_tools_tab/variant_table/multiselection_of_variants_and_bulk_actions_-340+.md) - [Manually add variants to a delivered case](/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab/analysis_tools_tab/variant_table/manually_add_variants_to_a_delivered_case.md) - [Download variants](/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab/analysis_tools_tab/variant_table/download_variants.md) - [Filters/Presets panel](/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab/analysis_tools_tab/filters_presets_panel.md) - [Variant search](/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab/analysis_tools_tab/filters_presets_panel/variant_search.md) - [Filters](/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab/analysis_tools_tab/filters_presets_panel/filters.md) - [v100.40.0+ filter list](/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab/analysis_tools_tab/filters_presets_panel/filters/v100.40.0+-filter-list.md) - [Quality filters](/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab/analysis_tools_tab/filters_presets_panel/filters/quality_filters.md) - [Polymorphism filters](/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab/analysis_tools_tab/filters_presets_panel/filters/polymorphism_filters.md) - [Variant type filters](/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab/analysis_tools_tab/filters_presets_panel/filters/variant_type_filters.md) - [Variant effect filters](/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab/analysis_tools_tab/filters_presets_panel/filters/variant_effect_filters.md) - [In silico predictions filters (v37.0+)](/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab/analysis_tools_tab/filters_presets_panel/filters/in-silico-predictions-filters.md) - [Gene filters](/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab/analysis_tools_tab/filters_presets_panel/filters/gene_filters.md) - [Phenomatch filters](/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab/analysis_tools_tab/filters_presets_panel/filters/phenomatch_filters.md) - [Inheritance filters](/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab/analysis_tools_tab/filters_presets_panel/filters/inheritance_filters.md) - [Zygosity filters](/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab/analysis_tools_tab/filters_presets_panel/filters/zygosity_filters.md) - [Evidence & Tags filters](/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab/analysis_tools_tab/filters_presets_panel/filters/user_filters.md) - [Presets](/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab/analysis_tools_tab/filters_presets_panel/presets.md) - [Analysis tools tab Beta (v100.39.0+)](/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab/analysis-tools-tab-beta-v100.39.0+.md) - [Viewing modes](/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab/analysis-tools-tab-beta-v100.39.0+/viewing-modes.md) - [Variant table](/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab/analysis-tools-tab-beta-v100.39.0+/variant_table.md) - [Filters/Presets panel](/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab/analysis-tools-tab-beta-v100.39.0+/filters_presets_panel.md) - [Filters](/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab/analysis-tools-tab-beta-v100.39.0+/filters_presets_panel/filters.md) - [Versions tab](/emedgene-analyze-manual/reviewing_a_case/versions_tab.md) - [Evidence page](/emedgene-analyze-manual/reviewing_a_case/evidence_page.md) - [Phenotypic match](/emedgene-analyze-manual/reviewing_a_case/phenotypic-match.md) - [Phenotypic match models](/emedgene-analyze-manual/reviewing_a_case/phenotypic-match/phenotypic-match-models.md) - [Phenotypic match strength](/emedgene-analyze-manual/reviewing_a_case/phenotypic-match/phenotypic_match_strength.md) - [Editing an existing case](/emedgene-analyze-manual/reviewing_a_case/editing_an_existing_case.md) - [Reflex genetic testing](/emedgene-analyze-manual/reviewing_a_case/reflex_genetic_testing.md) - [Variant zygosity notations](/emedgene-analyze-manual/reviewing_a_case/variant_zygosity_notations.md) - [STR calling and interpretation](/emedgene-analyze-manual/reviewing_a_case/str_calling_and_interpretation.md) - [Reviewing a variant](/emedgene-analyze-manual/variant_page.md) - [Variant page](/emedgene-analyze-manual/variant_page/variant_page.md) - [Variant page top bar](/emedgene-analyze-manual/variant_page/variant_page_top_bar.md) - [Variant tagging widget](/emedgene-analyze-manual/variant_page/variant_tagging_widget.md) - [Multiple tags](/emedgene-analyze-manual/variant_page/variant_tagging_widget/multiple-tags.md) - [Summary tab](/emedgene-analyze-manual/variant_page/summary_section.md) - [Clinical significance tab](/emedgene-analyze-manual/variant_page/clinical_significance_section.md) - [Variant info](/emedgene-analyze-manual/variant_page/clinical_significance_section/variant-info.md) - [Transcript](/emedgene-analyze-manual/variant_page/clinical_significance_section/variant-info/transcript.md) - [Resources](/emedgene-analyze-manual/variant_page/clinical_significance_section/variant-info/resources.md) - [In silico predictions](/emedgene-analyze-manual/variant_page/clinical_significance_section/in-silico-predictions.md) - [Gene metrics](/emedgene-analyze-manual/variant_page/clinical_significance_section/gene-metrics.md) - [Clinical significance](/emedgene-analyze-manual/variant_page/clinical_significance_section/clinical-significance.md) - [Gene-related diseases](/emedgene-analyze-manual/variant_page/clinical_significance_section/gene-related-diseases.md) - [Quality tab](/emedgene-analyze-manual/variant_page/quality_section.md) - [Visualization tab](/emedgene-analyze-manual/variant_page/visualization_section.md) - [Population statistics tab](/emedgene-analyze-manual/variant_page/population_statistics_section.md) - [Connected variants tab](/emedgene-analyze-manual/variant_page/connected-variants-tab.md) - [Related cases tab](/emedgene-analyze-manual/variant_page/related_cases_section.md) - [Network data view controls](/emedgene-analyze-manual/variant_page/related_cases_section/network-data-view-controls.md) - [Pathogenicity trend bar](/emedgene-analyze-manual/variant_page/related_cases_section/pathogenicity-trend-bar.md) - [Related cases table](/emedgene-analyze-manual/variant_page/related_cases_section/related-cases-table.md) - [CNV overlap percentage filter](/emedgene-analyze-manual/variant_page/related_cases_section/cnv_overlap_percentage.md) - [One-way CNV annotation overlap](/emedgene-analyze-manual/variant_page/related_cases_section/cnv_overlap_percentage/one-way-cnv-annotation-overlap.md) - [Evidence tab](/emedgene-analyze-manual/variant_page/evidence_section.md) - [ACMG SNV Classification wizard](/emedgene-analyze-manual/variant_page/evidence_section/acmg_snv_classification_wizard.md) - [Logic behind ACMG classification of SNVs](/emedgene-analyze-manual/variant_page/evidence_section/logic_behind_acmg_classification_of_snvs.md) - [Individual ACMG criteria evaluation](/emedgene-analyze-manual/variant_page/evidence_section/individual-acmg-criteria-evaluation.md) - [ACMG CNV Classification wizard](/emedgene-analyze-manual/variant_page/evidence_section/acmg_cnv_classification_wizard.md) - [Variant page sidebar](/emedgene-analyze-manual/variant_page/variant_page_sidebar_-229+.md) - [Case completion and reporting](/emedgene-analyze-manual/case-completion-and-reporting.md) - [Completing case interpretation](/emedgene-analyze-manual/case-completion-and-reporting/completing-case-interpretation.md) - [Finalizing a case](/emedgene-analyze-manual/case-completion-and-reporting/finalizing_a_case.md) - [Reporting](/emedgene-analyze-manual/case-completion-and-reporting/clinical_report.md) - [Variant visualization](/emedgene-analyze-manual/variant-visualization.md) - [Variant visualization tool](/emedgene-analyze-manual/variant-visualization/variant-visualization-tool.md) - [Viewing modes](/emedgene-analyze-manual/variant-visualization/variant-visualization-tool/viewing-modes.md) - [Visualization tracks](/emedgene-analyze-manual/variant-visualization/variant-visualization-tool/visualization-tracks.md) - [Visual aids](/emedgene-analyze-manual/variant-visualization/variant-visualization-tool/visual-aids.md) - [Manually add variant from IGV](/emedgene-analyze-manual/variant-visualization/variant-visualization-tool/manually-add-variant-from-igv.md) - [Variant visualization setup](/emedgene-analyze-manual/variant-visualization/variant_visualization_setup.md) - [Enabling visualization for a VCF case](/emedgene-analyze-manual/variant-visualization/variant_visualization_setup/enabling_visualization_for_a_vcf_case.md) - [Integration between Emedgene and desktop IGV](/emedgene-analyze-manual/variant-visualization/variant_visualization_setup/integration_between_emedgene_and_desktop_igv.md) - [Loading alignment files to your desktop IGV](/emedgene-analyze-manual/variant-visualization/variant_visualization_setup/loading_alignment_files_to_your_desktop_igv_-320+.md) - [Analyze Network](/emedgene-analyze-manual/analyze_network.md) - [Analyze Network Setup](/emedgene-analyze-manual/analyze_network/analyze_network_setup.md) - [Network sharing configuration](/emedgene-analyze-manual/analyze_network/network_sharing_configuration.md) - [Case subject consent for extended sharing](/emedgene-analyze-manual/analyze_network/case_subject_consent_for_extended_sharing.md) - [Public vs Private network](/emedgene-analyze-manual/analyze_network/public_vs_private_network.md) - [Create a network](/emedgene-analyze-manual/analyze_network/create_a_network.md) - [Set network data sharing policy](/emedgene-analyze-manual/analyze_network/set_network_data_sharing_policy.md) - [Leave a network](/emedgene-analyze-manual/analyze_network/leave_a_network.md) - [Delete a network](/emedgene-analyze-manual/analyze_network/delete_a_network.md) - [Settings](/emedgene-analyze-manual/settings.md) - [My settings](/emedgene-analyze-manual/settings/my_settings.md) - [Management](/emedgene-analyze-manual/settings/management.md) - [Illumina support access](/emedgene-analyze-manual/settings/management/illumina-support-access.md) - [Storage](/emedgene-analyze-manual/settings/management/storage.md) - [S3 credentials](/emedgene-analyze-manual/settings/management/s3-credentials.md) - [Case statuses](/emedgene-analyze-manual/settings/management/case-statuses.md) - [Test settings](/emedgene-analyze-manual/settings/management/test-settings.md) - [Groups](/emedgene-analyze-manual/settings/management/groups.md) - [Webhooks](/emedgene-analyze-manual/settings/management/webhooks.md) - [User access management](/emedgene-analyze-manual/settings/user_roles.md) - [User access management in Illumina environments](/emedgene-analyze-manual/settings/user_roles/user-access-management-in-illumina-environments.md) - [User access management in legacy Emedgene environments](/emedgene-analyze-manual/settings/user_roles/user-access-management-in-legacy-emedgene-environments.md) - [IAM scopes/Emedgene roles](/emedgene-analyze-manual/settings/user_roles/iam-scopes-emedgene-roles.md) - [Network](/emedgene-analyze-manual/settings/network.md) - [Organization settings](/emedgene-analyze-manual/settings/organization_settings_-330+.md) - [General](/emedgene-analyze-manual/settings/organization_settings_-330+/general.md): General settings and organization information - [Workbench & Pipeline](/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline.md) - [AI Shortlist module](/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/ai-shortlist-module.md) - [AI ACMG module (v100.39.0+)](/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/ai-acmg-module-v100.39.0+.md) - [Pipeline versions](/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/pipeline-versions.md) - [Organization DB management](/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/organization-db-management.md) - [Organization databases](/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/organization-db-management/organization-databases.md) - [Configuring an organization database](/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/organization-db-management/configuring-an-organization-database.md) - [Creating a database VCF file](/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/organization-db-management/configuring-an-organization-database/creating-a-database-vcf-file.md) - [Creating an internal database VCF file](/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/organization-db-management/configuring-an-organization-database/creating-a-database-vcf-file/creating-an-internal-database-vcf-file.md) - [Creating an external database VCF file](/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/organization-db-management/configuring-an-organization-database/creating-a-database-vcf-file/creating-an-external-database-vcf-file.md) - [Registering a database](/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/organization-db-management/configuring-an-organization-database/registering-a-database.md) - [Modifying database settings](/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/organization-db-management/configuring-an-organization-database/modifying-database-settings.md) - [SV annotation thresholds](/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/sv-annotation-thresholds.md) - [Environment](/emedgene-analyze-manual/settings/organization_settings_-330+/environment.md) - [Organization URL (ILMN clouds)](/emedgene-analyze-manual/settings/organization_settings_-330+/environment/organization-url-ilmn-clouds.md) - [Platform version](/emedgene-analyze-manual/settings/organization_settings_-330+/environment/platform-version.md) - [How do I check my platform version?](/emedgene-analyze-manual/settings/organization_settings_-330+/environment/platform-version/how_do_i_check_the_version_of_my_environment.md) - [Case identifier](/emedgene-analyze-manual/settings/organization_settings_-330+/environment/case-identifier.md) - [Default page](/emedgene-analyze-manual/settings/organization_settings_-330+/environment/default-page.md) - [Analysis tools columns order](/emedgene-analyze-manual/settings/organization_settings_-330+/environment/analysis-tools-columns-order.md) - [Case settings](/emedgene-analyze-manual/settings/organization_settings_-330+/case-settings.md) - [Variant tags](/emedgene-analyze-manual/settings/organization_settings_-330+/case-settings/variant-tags.md) - [Lab workflow](/emedgene-analyze-manual/settings/organization_settings_-330+/lab-workflow.md) - [Presets](/emedgene-analyze-manual/settings/organization_settings_-330+/lab-workflow/presets.md) - [Preset groups](/emedgene-analyze-manual/settings/organization_settings_-330+/lab-workflow/preset-groups.md) - [Default preset group](/emedgene-analyze-manual/settings/organization_settings_-330+/lab-workflow/default-preset-group.md) - [Kit Management](/emedgene-analyze-manual/settings/organization_settings_-330+/kit-management.md) - [BED files](/emedgene-analyze-manual/settings/organization_settings_-330+/kit-management/bed-files.md) - [Required format for a BED file defining a kit](/emedgene-analyze-manual/settings/organization_settings_-330+/kit-management/bed-files/what_is_the_required_format_for_a_bed_file_defining_a_kit.md) - [Panel of normals (PON)](/emedgene-analyze-manual/settings/organization_settings_-330+/kit-management/panel-of-normals-pon.md) - [Attaching a PON to a Coverage BED kit](/emedgene-analyze-manual/settings/organization_settings_-330+/kit-management/panel-of-normals-pon/attaching-a-pon-to-a-coverage-bed-kit.md) - [Removing PON files from storage](/emedgene-analyze-manual/settings/organization_settings_-330+/kit-management/panel-of-normals-pon/removing-pon-files-from-storage.md) - [Creating a PON for Emedgene using BaseSpace Baseline Builder](/emedgene-analyze-manual/settings/organization_settings_-330+/kit-management/panel-of-normals-pon/creating-a-pon-for-emedgene-using-basespace-baseline-builder.md) - [Quality parameters](/emedgene-analyze-manual/settings/organization_settings_-330+/quality-parameters-38.0+.md) - [NGS quality](/emedgene-analyze-manual/settings/organization_settings_-330+/quality-parameters-38.0+/ngs-quality.md) - [Array sample quality](/emedgene-analyze-manual/settings/organization_settings_-330+/quality-parameters-38.0+/array-sample-quality.md) - [Integration (v100.39.0+)](/emedgene-analyze-manual/settings/organization_settings_-330+/integration-v100.39.0+.md) - [Encryption settings](/emedgene-analyze-manual/settings/organization_settings_-330+/integration-v100.39.0+/encryption-settings.md) - [Integrations](/emedgene-analyze-manual/integrations.md) - [Automatic Case Creation from ICA - Cyto Array Analysis](/emedgene-analyze-manual/integrations/automatic-case-creation-from-ica-cyto-array-analysis.md): Seamless end-to-end workflow from scanner to tertiary analysis with no human intervention. - [API Beginner Guide](/emedgene-analyze-manual/integrations/api-beginner-guide.md) - [Advanced API Implementations](/emedgene-analyze-manual/integrations/advanced-api-implementations.md): This page provides several code examples demonstrating how to use the platform for common scenarios. While you don't need to follow or implement every example, they can serve as useful starting points - [API Key Generation](/emedgene-analyze-manual/integrations/api-key-generation.md) - [BSSH Integration](/emedgene-analyze-manual/integrations/bssh-integration.md): Please contact Tech Support with the subject "BaseSpace Emedgene Connect app" for assistance. - [ICA Integration](/emedgene-analyze-manual/integrations/ica-integration.md) - [Webhook Integration](/emedgene-analyze-manual/integrations/webhook-integration.md) - [Troubleshooting](/emedgene-analyze-manual/troubleshooting.md) - [Which browser should I use with Emedgene?](/emedgene-analyze-manual/troubleshooting/which_browser_should_i_use_with_emedgene.md) - [How do I use developer tools to collect logs?](/emedgene-analyze-manual/troubleshooting/how_do_i_use_developer_tools_to_collect_logs.md) - [Performance issues troubleshooting](/emedgene-analyze-manual/troubleshooting/performance_issue_troubleshooting.md)