CHANGELOG.md
LICENSE
MANIFEST.in
README.md
requirements-dev.txt
requirements.txt
setup.cfg
setup.py
scout/__init__.py
scout/__version__.py
scout/adapter/__init__.py
scout/adapter/client.py
scout/adapter/mongo/__init__.py
scout/adapter/mongo/acmg.py
scout/adapter/mongo/base.py
scout/adapter/mongo/case.py
scout/adapter/mongo/case_events.py
scout/adapter/mongo/case_group.py
scout/adapter/mongo/clinvar.py
scout/adapter/mongo/cytoband.py
scout/adapter/mongo/event.py
scout/adapter/mongo/filter.py
scout/adapter/mongo/hgnc.py
scout/adapter/mongo/hpo.py
scout/adapter/mongo/index.py
scout/adapter/mongo/institute.py
scout/adapter/mongo/managed_variant.py
scout/adapter/mongo/matchmaker.py
scout/adapter/mongo/omim.py
scout/adapter/mongo/panel.py
scout/adapter/mongo/phenomodel.py
scout/adapter/mongo/query.py
scout/adapter/mongo/rank_model.py
scout/adapter/mongo/transcript.py
scout/adapter/mongo/user.py
scout/adapter/mongo/variant.py
scout/adapter/mongo/variant_events.py
scout/adapter/mongo/variant_loader.py
scout/build/__init__.py
scout/build/acmg.py
scout/build/case.py
scout/build/disease.py
scout/build/hpo.py
scout/build/individual.py
scout/build/institute.py
scout/build/managed_variant.py
scout/build/panel.py
scout/build/phenotype.py
scout/build/user.py
scout/build/genes/__init__.py
scout/build/genes/exon.py
scout/build/genes/hgnc_gene.py
scout/build/genes/transcript.py
scout/build/variant/__init__.py
scout/build/variant/clnsig.py
scout/build/variant/compound.py
scout/build/variant/gene.py
scout/build/variant/genotype.py
scout/build/variant/transcript.py
scout/build/variant/variant.py
scout/commands/__init__.py
scout/commands/base.py
scout/commands/convert.py
scout/commands/index_command.py
scout/commands/serve.py
scout/commands/utils.py
scout/commands/wipe_database.py
scout/commands/delete/__init__.py
scout/commands/delete/delete_command.py
scout/commands/download/__init__.py
scout/commands/download/download_command.py
scout/commands/download/ensembl.py
scout/commands/download/everything.py
scout/commands/download/exac.py
scout/commands/download/hgnc.py
scout/commands/download/hpo.py
scout/commands/download/omim.py
scout/commands/export/__init__.py
scout/commands/export/case.py
scout/commands/export/database.py
scout/commands/export/exon.py
scout/commands/export/export_command.py
scout/commands/export/export_handler.py
scout/commands/export/gene.py
scout/commands/export/hpo.py
scout/commands/export/mitochondrial_report.py
scout/commands/export/panel.py
scout/commands/export/transcript.py
scout/commands/export/utils.py
scout/commands/export/variant.py
scout/commands/load/__init__.py
scout/commands/load/base.py
scout/commands/load/case.py
scout/commands/load/cytoband.py
scout/commands/load/exons.py
scout/commands/load/institute.py
scout/commands/load/panel.py
scout/commands/load/region.py
scout/commands/load/report.py
scout/commands/load/research.py
scout/commands/load/user.py
scout/commands/load/variants.py
scout/commands/setup/__init__.py
scout/commands/setup/setup_scout.py
scout/commands/update/__init__.py
scout/commands/update/base.py
scout/commands/update/case.py
scout/commands/update/compounds.py
scout/commands/update/disease.py
scout/commands/update/genes.py
scout/commands/update/hpo.py
scout/commands/update/individual.py
scout/commands/update/institute.py
scout/commands/update/omim.py
scout/commands/update/panel.py
scout/commands/update/panelapp.py
scout/commands/update/phenotype_groups.py
scout/commands/update/user.py
scout/commands/view/__init__.py
scout/commands/view/aliases.py
scout/commands/view/base.py
scout/commands/view/case.py
scout/commands/view/collections.py
scout/commands/view/diseases.py
scout/commands/view/hgnc.py
scout/commands/view/hpo.py
scout/commands/view/index.py
scout/commands/view/individuals.py
scout/commands/view/institutes.py
scout/commands/view/intervals.py
scout/commands/view/panels.py
scout/commands/view/transcripts.py
scout/commands/view/users.py
scout/constants/__init__.py
scout/constants/acmg.py
scout/constants/case_tags.py
scout/constants/clinvar.py
scout/constants/clnsig.py
scout/constants/file_types.py
scout/constants/filters.py
scout/constants/gene_tags.py
scout/constants/igv_tracks.py
scout/constants/indexes.py
scout/constants/phenotype.py
scout/constants/query_terms.py
scout/constants/so_terms.py
scout/constants/variant_tags.py
scout/constants/variants_export.py
scout/demo/643594.clinical.SV.vcf.gz
scout/demo/643594.clinical.SV.vcf.gz.tbi
scout/demo/643594.clinical.str.annotated.limits.vcf.gz
scout/demo/643594.clinical.str.annotated.limits.vcf.gz.tbi
scout/demo/643594.clinical.str.annotated.vcf.gz
scout/demo/643594.clinical.str.annotated.vcf.gz.tbi
scout/demo/643594.clinical.str.stranger.vcf.gz
scout/demo/643594.clinical.str.stranger.vcf.gz.tbi
scout/demo/643594.clinical.str.vcf.gz
scout/demo/643594.clinical.str.vcf.gz.tbi
scout/demo/643594.clinical.vcf.gz
scout/demo/643594.clinical.vcf.gz.tbi
scout/demo/643594.config.yaml
scout/demo/643594.ped
scout/demo/643594.ped_check.csv
scout/demo/643594.peddy.ped
scout/demo/643594.research.SV.vcf.gz
scout/demo/643594.research.SV.vcf.gz.tbi
scout/demo/643594.research.vcf.gz
scout/demo/643594.research.vcf.gz.tbi
scout/demo/643594.sex_check.csv
scout/demo/643594.solo.smn.tsv
scout/demo/643594_vcol_exe_ver.yaml
scout/demo/643595.clinical.SV.vcf.gz
scout/demo/643595.clinical.SV.vcf.gz.tbi
scout/demo/643595.clinical.str.stranger.vcf.gz
scout/demo/643595.clinical.str.stranger.vcf.gz.tbi
scout/demo/643595.clinical.vcf.gz
scout/demo/643595.clinical.vcf.gz.tbi
scout/demo/643595.config.yaml
scout/demo/999-99.test.cgh
scout/demo/ACC5963A1_lanes_1234_star_sorted_sj_filtered.bigWig
scout/demo/ACC5963A1_lanes_1234_star_sorted_sj_filtered_sorted.bed.gz
scout/demo/ACC5963A1_lanes_1234_star_sorted_sj_filtered_sorted.bed.gz.tbi
scout/demo/ADM1059A1.test.cgh
scout/demo/ADM1059A2.test.cgh
scout/demo/ADM1059A3.test.cgh
scout/demo/__init__.py
scout/demo/cancer.load_config.yaml
scout/demo/cancer_cnv_report.pdf
scout/demo/cancer_coverage_qc_report.html
scout/demo/cancer_test.ped
scout/demo/cancer_test.vcf.gz
scout/demo/cancer_test.vcf.gz.tbi
scout/demo/chanjo4_demo.sql
scout/demo/customannotations_one.vcf.gz
scout/demo/customannotations_one.vcf.gz.tbi
scout/demo/delivery_report.html
scout/demo/draw-fusions-example.pdf
scout/demo/empty.clinical.SV.vcf.gz
scout/demo/empty.clinical.SV.vcf.gz.tbi
scout/demo/madeline.xml
scout/demo/manta_vep_94_annotated_sv_cancer_file.vcf.gz
scout/demo/panel_1.csv
scout/demo/panel_1.txt
scout/demo/panelapp_test_panel.json
scout/demo/reduced_mt.bam
scout/demo/reduced_mt.bam.bai
scout/demo/reference_info.yaml
scout/demo/rnafusion.load_config.yaml
scout/demo/rnafusion_inspector_example.html
scout/demo/rnafusion_report_example.html
scout/demo/scout_example_tumor_only.SV.CNV.sorted.vcf.gz
scout/demo/scout_example_tumor_only.SV.CNV.sorted.vcf.gz.tbi
scout/demo/scout_example_tumor_only.snv.indel.sorted.vcf.gz
scout/demo/scout_example_tumor_only.snv.indel.sorted.vcf.gz.tbi
scout/demo/vep104_annotated.vcf
scout/demo/vep97_annotated_clnsig_conservation_revel.vcf
scout/demo/REViewer_test_data/catalog_test.json
scout/demo/REViewer_test_data/justhusky_exphun_hugelymodelbat.vcf
scout/demo/REViewer_test_data/justhusky_exphun_hugelymodelbat_realigned.bam
scout/demo/REViewer_test_data/justhusky_exphun_hugelymodelbat_realigned.bam.bai
scout/demo/images/chromograph_demo/autozygous_regions1.png
scout/demo/images/chromograph_demo/autozygous_regions10.png
scout/demo/images/chromograph_demo/autozygous_regions11.png
scout/demo/images/chromograph_demo/autozygous_regions12.png
scout/demo/images/chromograph_demo/autozygous_regions13.png
scout/demo/images/chromograph_demo/autozygous_regions14.png
scout/demo/images/chromograph_demo/autozygous_regions15.png
scout/demo/images/chromograph_demo/autozygous_regions16.png
scout/demo/images/chromograph_demo/autozygous_regions17.png
scout/demo/images/chromograph_demo/autozygous_regions18.png
scout/demo/images/chromograph_demo/autozygous_regions19.png
scout/demo/images/chromograph_demo/autozygous_regions2.png
scout/demo/images/chromograph_demo/autozygous_regions20.png
scout/demo/images/chromograph_demo/autozygous_regions21.png
scout/demo/images/chromograph_demo/autozygous_regions22.png
scout/demo/images/chromograph_demo/autozygous_regions3.png
scout/demo/images/chromograph_demo/autozygous_regions4.png
scout/demo/images/chromograph_demo/autozygous_regions5.png
scout/demo/images/chromograph_demo/autozygous_regions6.png
scout/demo/images/chromograph_demo/autozygous_regions7.png
scout/demo/images/chromograph_demo/autozygous_regions8.png
scout/demo/images/chromograph_demo/autozygous_regions9.png
scout/demo/images/chromograph_demo/autozygous_regionsM.png
scout/demo/images/chromograph_demo/autozygous_regionsX.png
scout/demo/images/chromograph_demo/autozygous_regionsY.png
scout/demo/images/chromograph_demo/coverage1.png
scout/demo/images/chromograph_demo/coverage10.png
scout/demo/images/chromograph_demo/coverage11.png
scout/demo/images/chromograph_demo/coverage12.png
scout/demo/images/chromograph_demo/coverage13.png
scout/demo/images/chromograph_demo/coverage14.png
scout/demo/images/chromograph_demo/coverage15.png
scout/demo/images/chromograph_demo/coverage16.png
scout/demo/images/chromograph_demo/coverage17.png
scout/demo/images/chromograph_demo/coverage18.png
scout/demo/images/chromograph_demo/coverage19.png
scout/demo/images/chromograph_demo/coverage2.png
scout/demo/images/chromograph_demo/coverage20.png
scout/demo/images/chromograph_demo/coverage21.png
scout/demo/images/chromograph_demo/coverage22.png
scout/demo/images/chromograph_demo/coverage3.png
scout/demo/images/chromograph_demo/coverage4.png
scout/demo/images/chromograph_demo/coverage5.png
scout/demo/images/chromograph_demo/coverage6.png
scout/demo/images/chromograph_demo/coverage7.png
scout/demo/images/chromograph_demo/coverage8.png
scout/demo/images/chromograph_demo/coverage9.png
scout/demo/images/chromograph_demo/coverageM.png
scout/demo/images/chromograph_demo/coverageX.png
scout/demo/images/chromograph_demo/coverageY.png
scout/demo/images/chromograph_demo/upd_regions1.png
scout/demo/images/chromograph_demo/upd_regions10.png
scout/demo/images/chromograph_demo/upd_regions11.png
scout/demo/images/chromograph_demo/upd_regions12.png
scout/demo/images/chromograph_demo/upd_regions13.png
scout/demo/images/chromograph_demo/upd_regions14.png
scout/demo/images/chromograph_demo/upd_regions15.png
scout/demo/images/chromograph_demo/upd_regions16.png
scout/demo/images/chromograph_demo/upd_regions17.png
scout/demo/images/chromograph_demo/upd_regions18.png
scout/demo/images/chromograph_demo/upd_regions19.png
scout/demo/images/chromograph_demo/upd_regions2.png
scout/demo/images/chromograph_demo/upd_regions20.png
scout/demo/images/chromograph_demo/upd_regions21.png
scout/demo/images/chromograph_demo/upd_regions22.png
scout/demo/images/chromograph_demo/upd_regions3.png
scout/demo/images/chromograph_demo/upd_regions4.png
scout/demo/images/chromograph_demo/upd_regions5.png
scout/demo/images/chromograph_demo/upd_regions6.png
scout/demo/images/chromograph_demo/upd_regions7.png
scout/demo/images/chromograph_demo/upd_regions8.png
scout/demo/images/chromograph_demo/upd_regions9.png
scout/demo/images/chromograph_demo/upd_regionsM.png
scout/demo/images/chromograph_demo/upd_regionsX.png
scout/demo/images/chromograph_demo/upd_regionsY.png
scout/demo/images/chromograph_demo/upd_sites_1.png
scout/demo/images/chromograph_demo/upd_sites_10.png
scout/demo/images/chromograph_demo/upd_sites_11.png
scout/demo/images/chromograph_demo/upd_sites_12.png
scout/demo/images/chromograph_demo/upd_sites_13.png
scout/demo/images/chromograph_demo/upd_sites_14.png
scout/demo/images/chromograph_demo/upd_sites_15.png
scout/demo/images/chromograph_demo/upd_sites_16.png
scout/demo/images/chromograph_demo/upd_sites_17.png
scout/demo/images/chromograph_demo/upd_sites_18.png
scout/demo/images/chromograph_demo/upd_sites_19.png
scout/demo/images/chromograph_demo/upd_sites_2.png
scout/demo/images/chromograph_demo/upd_sites_20.png
scout/demo/images/chromograph_demo/upd_sites_21.png
scout/demo/images/chromograph_demo/upd_sites_22.png
scout/demo/images/chromograph_demo/upd_sites_3.png
scout/demo/images/chromograph_demo/upd_sites_4.png
scout/demo/images/chromograph_demo/upd_sites_5.png
scout/demo/images/chromograph_demo/upd_sites_6.png
scout/demo/images/chromograph_demo/upd_sites_7.png
scout/demo/images/chromograph_demo/upd_sites_8.png
scout/demo/images/chromograph_demo/upd_sites_9.png
scout/demo/images/chromograph_demo/upd_sites_M.png
scout/demo/images/chromograph_demo/upd_sites_X.png
scout/demo/images/chromograph_demo/upd_sites_Y.png
scout/demo/images/custom_images/640x480_AR.svg
scout/demo/images/custom_images/640x480_ATN1.svg
scout/demo/images/custom_images/640x480_one.png
scout/demo/images/custom_images/640x480_three.svg
scout/demo/images/custom_images/640x480_two.jpg
scout/demo/mitodel_test_files/earlycasualcaiman_lanes_1_sorted_md_mitodel.txt
scout/demo/mitodel_test_files/hugelymodelbat_lanes_1_sorted_md_mitodel.txt
scout/demo/mitodel_test_files/slowlycivilbuck_lanes_1_sorted_md_mitodel.txt
scout/demo/resources/__init__.py
scout/demo/resources/chanjo4_structure.sql
scout/demo/resources/ensembl_exons_37_reduced.txt
scout/demo/resources/ensembl_exons_38_reduced.txt
scout/demo/resources/ensembl_genes_37_reduced.txt
scout/demo/resources/ensembl_genes_38_reduced.txt
scout/demo/resources/ensembl_transcripts_37_reduced.txt
scout/demo/resources/ensembl_transcripts_38_reduced.txt
scout/demo/resources/forweb_cleaned_exac_r03_march16_z_data_pLI_reduced.txt
scout/demo/resources/genemap2_reduced.txt
scout/demo/resources/genes_to_phenotype_reduced.txt
scout/demo/resources/hgnc_reduced_set.txt
scout/demo/resources/hpo_terms.csv
scout/demo/resources/mim2gene_reduced.txt
scout/demo/resources/phenotype_to_genes_reduced.txt
scout/demo/resources/reduced.hpo.obo
scout/exceptions/__init__.py
scout/exceptions/config.py
scout/exceptions/database.py
scout/exceptions/pedigree.py
scout/exceptions/vcf.py
scout/export/__init__.py
scout/export/exon.py
scout/export/gene.py
scout/export/panel.py
scout/export/transcript.py
scout/export/variant.py
scout/load/__init__.py
scout/load/all.py
scout/load/case.py
scout/load/cytoband.py
scout/load/exon.py
scout/load/hgnc_gene.py
scout/load/hpo.py
scout/load/institute.py
scout/load/panel.py
scout/load/report.py
scout/load/setup.py
scout/load/transcript.py
scout/log/__init__.py
scout/log/handlers.py
scout/log/log.py
scout/models/__init__.py
scout/models/acmg_evaluation.py
scout/models/clinvar.py
scout/models/event.py
scout/models/hgnc_map.py
scout/models/institute.py
scout/models/managed_variant.py
scout/models/panel.py
scout/models/phenomodel.py
scout/models/phenotype_term.py
scout/models/user.py
scout/models/case/__init__.py
scout/models/case/case.py
scout/models/variant/__init__.py
scout/models/variant/gene.py
scout/models/variant/transcript.py
scout/models/variant/variant.py
scout/parse/__init__.py
scout/parse/case.py
scout/parse/cytoband.py
scout/parse/ensembl.py
scout/parse/exac.py
scout/parse/hgnc.py
scout/parse/hpo_mappings.py
scout/parse/hpo_terms.py
scout/parse/matchmaker.py
scout/parse/mitodel.py
scout/parse/models.py
scout/parse/omim.py
scout/parse/panel.py
scout/parse/peddy.py
scout/parse/smn.py
scout/parse/variant/__init__.py
scout/parse/variant/callers.py
scout/parse/variant/clnsig.py
scout/parse/variant/compound.py
scout/parse/variant/conservation.py
scout/parse/variant/coordinates.py
scout/parse/variant/deleteriousness.py
scout/parse/variant/frequency.py
scout/parse/variant/gene.py
scout/parse/variant/genotype.py
scout/parse/variant/headers.py
scout/parse/variant/ids.py
scout/parse/variant/managed_variant.py
scout/parse/variant/models.py
scout/parse/variant/rank_score.py
scout/parse/variant/transcript.py
scout/parse/variant/variant.py
scout/resources/__init__.py
scout/resources/cytoBand_hg19.txt.gz
scout/resources/cytoBand_hg38.txt.gz
scout/server/__init__.py
scout/server/app.py
scout/server/auto.py
scout/server/config.py
scout/server/links.py
scout/server/utils.py
scout/server/blueprints/__init__.py
scout/server/blueprints/alignviewers/__init__.py
scout/server/blueprints/alignviewers/controllers.py
scout/server/blueprints/alignviewers/partial.py
scout/server/blueprints/alignviewers/views.py
scout/server/blueprints/alignviewers/templates/alignviewers/igv_sashimi_viewer.html
scout/server/blueprints/alignviewers/templates/alignviewers/igv_viewer.html
scout/server/blueprints/alignviewers/templates/alignviewers/utils.html
scout/server/blueprints/api/__init__.py
scout/server/blueprints/api/views.py
scout/server/blueprints/cases/__init__.py
scout/server/blueprints/cases/controllers.py
scout/server/blueprints/cases/views.py
scout/server/blueprints/cases/static/case_images.js
scout/server/blueprints/cases/static/case_styles.css
scout/server/blueprints/cases/static/edit_pedigree.js
scout/server/blueprints/cases/static/madeline.js
scout/server/blueprints/cases/templates/cases/case.html
scout/server/blueprints/cases/templates/cases/case_report.html
scout/server/blueprints/cases/templates/cases/case_sma.html
scout/server/blueprints/cases/templates/cases/clinvar.html
scout/server/blueprints/cases/templates/cases/collapsible_actionbar.html
scout/server/blueprints/cases/templates/cases/diseases.html
scout/server/blueprints/cases/templates/cases/gene_panel.html
scout/server/blueprints/cases/templates/cases/index.html
scout/server/blueprints/cases/templates/cases/individuals_table.html
scout/server/blueprints/cases/templates/cases/institutes_sidebar.html
scout/server/blueprints/cases/templates/cases/matchmaker.html
scout/server/blueprints/cases/templates/cases/phenotype.html
scout/server/blueprints/cases/templates/cases/utils.html
scout/server/blueprints/clinvar/__init__.py
scout/server/blueprints/clinvar/controllers.py
scout/server/blueprints/clinvar/form.py
scout/server/blueprints/clinvar/views.py
scout/server/blueprints/clinvar/static/form_style.css
scout/server/blueprints/clinvar/templates/clinvar_submissions.html
scout/server/blueprints/clinvar/templates/multistep_add_variant.html
scout/server/blueprints/dashboard/__init__.py
scout/server/blueprints/dashboard/controllers.py
scout/server/blueprints/dashboard/forms.py
scout/server/blueprints/dashboard/views.py
scout/server/blueprints/dashboard/static/charts.js
scout/server/blueprints/dashboard/templates/dashboard/dashboard_general.html
scout/server/blueprints/diagnoses/__init__.py
scout/server/blueprints/diagnoses/controllers.py
scout/server/blueprints/diagnoses/views.py
scout/server/blueprints/diagnoses/templates/diagnoses/omim_term.html
scout/server/blueprints/diagnoses/templates/diagnoses/omim_terms.html
scout/server/blueprints/genes/__init__.py
scout/server/blueprints/genes/controllers.py
scout/server/blueprints/genes/views.py
scout/server/blueprints/genes/templates/genes/gene.html
scout/server/blueprints/genes/templates/genes/genes.html
scout/server/blueprints/genes/templates/genes/layout.html
scout/server/blueprints/institutes/__init__.py
scout/server/blueprints/institutes/controllers.py
scout/server/blueprints/institutes/forms.py
scout/server/blueprints/institutes/views.py
scout/server/blueprints/institutes/static/form_scripts.js
scout/server/blueprints/institutes/static/timeline_styles.css
scout/server/blueprints/institutes/static/variants_list_scripts.js
scout/server/blueprints/institutes/templates/overview/cases.html
scout/server/blueprints/institutes/templates/overview/causatives.html
scout/server/blueprints/institutes/templates/overview/filters.html
scout/server/blueprints/institutes/templates/overview/gene_variants.html
scout/server/blueprints/institutes/templates/overview/institute_settings.html
scout/server/blueprints/institutes/templates/overview/institute_sidebar.html
scout/server/blueprints/institutes/templates/overview/phenomodel.html
scout/server/blueprints/institutes/templates/overview/phenomodels.html
scout/server/blueprints/institutes/templates/overview/timeline.html
scout/server/blueprints/institutes/templates/overview/users.html
scout/server/blueprints/institutes/templates/overview/utils.html
scout/server/blueprints/institutes/templates/overview/verified.html
scout/server/blueprints/login/__init__.py
scout/server/blueprints/login/controllers.py
scout/server/blueprints/login/models.py
scout/server/blueprints/login/views.py
scout/server/blueprints/login/static/aspirant.svg
scout/server/blueprints/login/static/commander.svg
scout/server/blueprints/login/static/commissioner.svg
scout/server/blueprints/login/static/constable.svg
scout/server/blueprints/login/static/dick_tracy.svg
scout/server/blueprints/login/static/inspector.svg
scout/server/blueprints/login/static/sergeant.svg
scout/server/blueprints/login/static/superintendent.svg
scout/server/blueprints/login/templates/login/users.html
scout/server/blueprints/managed_variants/__init__.py
scout/server/blueprints/managed_variants/controllers.py
scout/server/blueprints/managed_variants/forms.py
scout/server/blueprints/managed_variants/views.py
scout/server/blueprints/managed_variants/templates/managed_variants/managed_variants.html
scout/server/blueprints/panels/__init__.py
scout/server/blueprints/panels/controllers.py
scout/server/blueprints/panels/forms.py
scout/server/blueprints/panels/views.py
scout/server/blueprints/panels/templates/panels/gene-edit.html
scout/server/blueprints/panels/templates/panels/panel.html
scout/server/blueprints/panels/templates/panels/panel_pdf_case_hits.html
scout/server/blueprints/panels/templates/panels/panel_pdf_simple.html
scout/server/blueprints/panels/templates/panels/panels.html
scout/server/blueprints/phenotypes/__init__.py
scout/server/blueprints/phenotypes/controllers.py
scout/server/blueprints/phenotypes/views.py
scout/server/blueprints/phenotypes/templates/phenotypes/hpo_terms.html
scout/server/blueprints/public/__init__.py
scout/server/blueprints/public/views.py
scout/server/blueprints/public/static/GMS-logo-dark.png
scout/server/blueprints/public/static/file-earmark-x.svg
scout/server/blueprints/public/static/logo-gms.png
scout/server/blueprints/public/static/logo-karolinska-srgb.jpg
scout/server/blueprints/public/static/logo-karolinska.png
scout/server/blueprints/public/static/logo-lund-university-hospital.png
scout/server/blueprints/public/static/logo-scilifelab.png
scout/server/blueprints/public/static/scout-logo.png
scout/server/blueprints/public/static/swedac-1926-iso17025.png
scout/server/blueprints/public/static/ideograms/chromosome-1.png
scout/server/blueprints/public/static/ideograms/chromosome-10.png
scout/server/blueprints/public/static/ideograms/chromosome-11.png
scout/server/blueprints/public/static/ideograms/chromosome-12.png
scout/server/blueprints/public/static/ideograms/chromosome-13.png
scout/server/blueprints/public/static/ideograms/chromosome-14.png
scout/server/blueprints/public/static/ideograms/chromosome-15.png
scout/server/blueprints/public/static/ideograms/chromosome-16.png
scout/server/blueprints/public/static/ideograms/chromosome-17.png
scout/server/blueprints/public/static/ideograms/chromosome-18.png
scout/server/blueprints/public/static/ideograms/chromosome-19.png
scout/server/blueprints/public/static/ideograms/chromosome-2.png
scout/server/blueprints/public/static/ideograms/chromosome-20.png
scout/server/blueprints/public/static/ideograms/chromosome-21.png
scout/server/blueprints/public/static/ideograms/chromosome-22.png
scout/server/blueprints/public/static/ideograms/chromosome-3.png
scout/server/blueprints/public/static/ideograms/chromosome-4.png
scout/server/blueprints/public/static/ideograms/chromosome-5.png
scout/server/blueprints/public/static/ideograms/chromosome-6.png
scout/server/blueprints/public/static/ideograms/chromosome-7.png
scout/server/blueprints/public/static/ideograms/chromosome-8.png
scout/server/blueprints/public/static/ideograms/chromosome-9.png
scout/server/blueprints/public/static/ideograms/chromosome-M.png
scout/server/blueprints/public/static/ideograms/chromosome-X.png
scout/server/blueprints/public/static/ideograms/chromosome-Y.png
scout/server/blueprints/public/templates/public/index.html
scout/server/blueprints/variant/__init__.py
scout/server/blueprints/variant/controllers.py
scout/server/blueprints/variant/utils.py
scout/server/blueprints/variant/verification_controllers.py
scout/server/blueprints/variant/views.py
scout/server/blueprints/variant/templates/variant/acmg.html
scout/server/blueprints/variant/templates/variant/buttons.html
scout/server/blueprints/variant/templates/variant/cancer-variant.html
scout/server/blueprints/variant/templates/variant/components.html
scout/server/blueprints/variant/templates/variant/gene_disease_relations.html
scout/server/blueprints/variant/templates/variant/rank_score_results.html
scout/server/blueprints/variant/templates/variant/sanger.html
scout/server/blueprints/variant/templates/variant/str-variant-reviewer.html
scout/server/blueprints/variant/templates/variant/sv-variant.html
scout/server/blueprints/variant/templates/variant/tx_overview.html
scout/server/blueprints/variant/templates/variant/utils.html
scout/server/blueprints/variant/templates/variant/variant.html
scout/server/blueprints/variant/templates/variant/variant_details.html
scout/server/blueprints/variants/__init__.py
scout/server/blueprints/variants/controllers.py
scout/server/blueprints/variants/forms.py
scout/server/blueprints/variants/views.py
scout/server/blueprints/variants/static/form_scripts.js
scout/server/blueprints/variants/templates/variants/cancer-sv-variants.html
scout/server/blueprints/variants/templates/variants/cancer-variants.html
scout/server/blueprints/variants/templates/variants/components.html
scout/server/blueprints/variants/templates/variants/indicators.html
scout/server/blueprints/variants/templates/variants/str-variants.html
scout/server/blueprints/variants/templates/variants/sv-variants.html
scout/server/blueprints/variants/templates/variants/utils.html
scout/server/blueprints/variants/templates/variants/variants.html
scout/server/extensions/__init__.py
scout/server/extensions/beacon_extension.py
scout/server/extensions/clinvar_extension.py
scout/server/extensions/gens_extension.py
scout/server/extensions/ldap_extension.py
scout/server/extensions/loqus_extension.py
scout/server/extensions/matchmaker_extension.py
scout/server/extensions/mongo_extension.py
scout/server/extensions/phenopacket_extension.py
scout/server/extensions/rerunner_extension.py
scout/server/static/bs_styles.css
scout/server/static/favicon.ico
scout/server/static/humans.txt
scout/server/static/robots.txt
scout/server/templates/bootstrap_global.html
scout/server/templates/layout.html
scout/server/templates/report_base.html
scout/server/templates/utils.html
scout/server/translations/sv/LC_MESSAGES/messages.mo
scout/server/translations/sv/LC_MESSAGES/messages.po
scout/update/__init__.py
scout/update/panel.py
scout/utils/__init__.py
scout/utils/acmg.py
scout/utils/algorithms.py
scout/utils/cloud_resources.py
scout/utils/convert.py
scout/utils/coordinates.py
scout/utils/date.py
scout/utils/dict_utils.py
scout/utils/ensembl_rest_clients.py
scout/utils/gene.py
scout/utils/handle.py
scout/utils/hgvs.py
scout/utils/link.py
scout/utils/md5.py
scout/utils/scout_requests.py
scout_browser.egg-info/PKG-INFO
scout_browser.egg-info/SOURCES.txt
scout_browser.egg-info/dependency_links.txt
scout_browser.egg-info/entry_points.txt
scout_browser.egg-info/not-zip-safe
scout_browser.egg-info/requires.txt
scout_browser.egg-info/top_level.txt
tests/conftest.py
tests/adapter/conftest.py
tests/adapter/mongo/test_base.py
tests/adapter/mongo/test_case_events.py
tests/adapter/mongo/test_case_group_handling.py
tests/adapter/mongo/test_case_handling.py
tests/adapter/mongo/test_comment_handling.py
tests/adapter/mongo/test_connect.py
tests/adapter/mongo/test_cytoband.py
tests/adapter/mongo/test_diagnosis_handler.py
tests/adapter/mongo/test_evaluated_variants.py
tests/adapter/mongo/test_event_handling.py
tests/adapter/mongo/test_gene_handler.py
tests/adapter/mongo/test_hpo_handler.py
tests/adapter/mongo/test_index_handling.py
tests/adapter/mongo/test_institute_handler.py
tests/adapter/mongo/test_load_adapter_case.py
tests/adapter/mongo/test_matchmaker.py
tests/adapter/mongo/test_panel_handler.py
tests/adapter/mongo/test_query.py
tests/adapter/mongo/test_rank_model.py
tests/adapter/mongo/test_sanger_validation.py
tests/adapter/mongo/test_transcript_handler.py
tests/adapter/mongo/test_update_synopsis
tests/adapter/mongo/test_user_handling.py
tests/adapter/mongo/test_variant_events.py
tests/adapter/mongo/test_variant_handling.py
tests/adapter/mongo/test_variant_loader.py
tests/build/conftest.py
tests/build/test_build_case.py
tests/build/test_build_clnsig.py
tests/build/test_build_disease.py
tests/build/test_build_exon.py
tests/build/test_build_gene.py
tests/build/test_build_hgnc_gene.py
tests/build/test_build_hgnc_transcript.py
tests/build/test_build_hpo.py
tests/build/test_build_individual.py
tests/build/test_build_institute.py
tests/build/test_build_panel.py
tests/build/test_build_user.py
tests/build/test_build_variant.py
tests/commands/conftest.py
tests/commands/test_base_command.py
tests/commands/test_convert_cmd.py
tests/commands/test_delete_case_cmd.py
tests/commands/test_index_cmd.py
tests/commands/test_serve_cmd.py
tests/commands/test_setup_cmd.py
tests/commands/test_wipe_database.py
tests/commands/delete/test_delete_cmd.py
tests/commands/download/test_download_ensembl_cmd.py
tests/commands/download/test_download_exac_cmd.py
tests/commands/download/test_download_hgnc_cmd.py
tests/commands/download/test_download_hpo_cmd.py
tests/commands/download/test_download_omim_cmd.py
tests/commands/export/test_export_cases_cmd.py
tests/commands/export/test_export_exons.py
tests/commands/export/test_export_gene.py
tests/commands/export/test_export_hpo_cmd.py
tests/commands/export/test_export_mt_report_cmd.py
tests/commands/export/test_export_panel_cmd.py
tests/commands/export/test_export_transcripts_cmd.py
tests/commands/export/test_export_variant_cmd.py
tests/commands/load/test_load_case_cmd.py
tests/commands/load/test_load_cnv_report_cmd.py
tests/commands/load/test_load_coverage_qc_report_cmd.py
tests/commands/load/test_load_cytoband_cmd.py
tests/commands/load/test_load_delivery_report_cmd.py
tests/commands/load/test_load_exons_cmd.py
tests/commands/load/test_load_institute_cmd.py
tests/commands/load/test_load_panel_cmd.py
tests/commands/load/test_load_region_cmd.py
tests/commands/load/test_load_report_cmd.py
tests/commands/load/test_load_research_cmd.py
tests/commands/load/test_load_user_cmd.py
tests/commands/load/test_load_variants_cmd.py
tests/commands/update/test_update_case_cmd.py
tests/commands/update/test_update_compounds_cli.py
tests/commands/update/test_update_disease_cmd.py
tests/commands/update/test_update_genes_cmd.py
tests/commands/update/test_update_groups_cmd.py
tests/commands/update/test_update_hpo_cmd.py
tests/commands/update/test_update_individual_cmd.py
tests/commands/update/test_update_institute_cmd.py
tests/commands/update/test_update_omim_cmd.py
tests/commands/update/test_update_panel_cmd.py
tests/commands/update/test_update_panelapp_green.py
tests/commands/update/test_update_user_cmd.py
tests/commands/view/test_panels_cmd.py
tests/commands/view/test_view_aliases_cmd.py
tests/commands/view/test_view_cases.py
tests/commands/view/test_view_cases_cmd.py
tests/commands/view/test_view_collections_cmd.py
tests/commands/view/test_view_diseases_cmd.py
tests/commands/view/test_view_hgnc.py
tests/commands/view/test_view_hpo_cmd.py
tests/commands/view/test_view_index_cmd.py
tests/commands/view/test_view_individuals_cmd.py
tests/commands/view/test_view_institutes_cmd.py
tests/commands/view/test_view_intervals_cmd.py
tests/commands/view/test_view_transcripts_cmd.py
tests/commands/view/test_view_users_cmd.py
tests/export/test_export_variants.py
tests/fixtures/bams/reduced_mt.bam
tests/fixtures/peds/clinvar.ped
tests/fixtures/vcfs/clinvar.vcf
tests/fixtures/vcfs/no_clinvar.vcf
tests/load/test_load_case.py
tests/load/test_load_exons.py
tests/load/test_load_hgnc_genes.py
tests/load/test_load_hpo.py
tests/load/test_load_institute.py
tests/load/test_load_panel.py
tests/load/test_load_transcripts.py
tests/load/test_load_variant.py
tests/load/test_setup_scout.py
tests/parse/conftest.py
tests/parse/test_frequency.py
tests/parse/test_ids.py
tests/parse/test_parse_callers.py
tests/parse/test_parse_case.py
tests/parse/test_parse_clnsig.py
tests/parse/test_parse_compounds.py
tests/parse/test_parse_conservation.py
tests/parse/test_parse_coordinates.py
tests/parse/test_parse_deleteriousness.py
tests/parse/test_parse_ensembl_exons.py
tests/parse/test_parse_ensembl_transcripts.py
tests/parse/test_parse_exac_genes.py
tests/parse/test_parse_genes.py
tests/parse/test_parse_genotype.py
tests/parse/test_parse_headers.py
tests/parse/test_parse_hgnc.py
tests/parse/test_parse_hpo_mappings.py
tests/parse/test_parse_hpo_terms.py
tests/parse/test_parse_managed_variant.py
tests/parse/test_parse_matchmaker.py
tests/parse/test_parse_omim.py
tests/parse/test_parse_panel.py
tests/parse/test_parse_rank_score.py
tests/parse/test_parse_transcripts.py
tests/parse/test_parse_variant.py
tests/parse/vcfs/one_cnvnator.vcf
tests/server/conftest.py
tests/server/test_links.py
tests/server/test_server_utils.py
tests/server/blueprints/alignviewers/test_alignviewers_controllers.py
tests/server/blueprints/alignviewers/test_alignviewers_views.py
tests/server/blueprints/api/test_api_views.py
tests/server/blueprints/cases/conftest.py
tests/server/blueprints/cases/test_cases_controllers.py
tests/server/blueprints/cases/test_cases_templates.py
tests/server/blueprints/cases/test_cases_utils.py
tests/server/blueprints/cases/test_cases_views.py
tests/server/blueprints/cases/test_matchmaker_controllers.py
tests/server/blueprints/clinvar/test_clinvar_views.py
tests/server/blueprints/dashboard/test_dashboard_controllers.py
tests/server/blueprints/dashboard/test_dashboard_views.py
tests/server/blueprints/diagnoses/test_diagnoses_views.py
tests/server/blueprints/genes/test_genes_views.py
tests/server/blueprints/institutes/test_institute_api.py
tests/server/blueprints/institutes/test_institute_controllers.py
tests/server/blueprints/institutes/test_institute_views.py
tests/server/blueprints/login/conftest.py
tests/server/blueprints/login/test_controllers.py
tests/server/blueprints/login/test_models.py
tests/server/blueprints/login/test_views.py
tests/server/blueprints/managed_variants/test_managed_variants_controllers.py
tests/server/blueprints/managed_variants/test_managed_variants_views.py
tests/server/blueprints/panels/test_panels_controllers.py
tests/server/blueprints/panels/test_panels_views.py
tests/server/blueprints/phenotypes/conftest.py
tests/server/blueprints/phenotypes/test_phenotypes_controllers.py
tests/server/blueprints/phenotypes/test_phenotypes_views.py
tests/server/blueprints/public/test_public_views.py
tests/server/blueprints/variant/test_variant_controllers.py
tests/server/blueprints/variant/test_variant_utils.py
tests/server/blueprints/variant/test_variant_verification_controllers.py
tests/server/blueprints/variant/test_variant_views.py
tests/server/blueprints/variants/test_variants_controllers.py
tests/server/blueprints/variants/test_variants_utils.py
tests/server/blueprints/variants/test_variants_views.py
tests/server/extensions/conftest.py
tests/server/extensions/test_beacon_extension.py
tests/server/extensions/test_execute_command.py
tests/server/extensions/test_gens_extension.py
tests/server/extensions/test_loqusdb_api_extension.py
tests/server/extensions/test_loqusdb_exe_extension.py
tests/server/extensions/test_matchmaker_extension.py
tests/server/extensions/test_phenopacket_extension.py
tests/server/extensions/test_rerunner_extension.py
tests/update/test_update_compounds.py
tests/update/test_update_institute.py
tests/update/test_update_panel.py
tests/utils/conftest.py
tests/utils/test_acmg.py
tests/utils/test_algorithms.py
tests/utils/test_cloud_resources.py
tests/utils/test_convert.py
tests/utils/test_date.py
tests/utils/test_dict_utils.py
tests/utils/test_ensembl_rest_clients.py
tests/utils/test_gene.py
tests/utils/test_hgvs.py
tests/utils/test_link_genes.py
tests/utils/test_par.py
tests/utils/test_scout_requests.py