scout-browser 4.89.1__py3-none-any.whl → 4.90__py3-none-any.whl

scout/constants/variant_tags.py

@@ -514,12 +514,67 @@ MOSAICISM_OPTIONS = {
 }
 
 VARIANTS_TARGET_FROM_CATEGORY = {
-    "sv": "variants.sv_variants",
     "cancer": "variants.cancer_variants",
     "cancer_sv": "variants.cancer_sv_variants",
+    "fusion": "variants.fusion_variants",
     "mei": "variants.mei_variants",
+    "outlier": "omics_variants.outliers",
     "snv": "variants.variants",
     "str": "variants.str_variants",
-    "fusion": "variants.fusion_variants",
-    "outlier": "omics_variants.outliers",
+    "sv": "variants.sv_variants",
+}
+
+_FREEBAYES = {"id": "freebayes", "name": "Freebayes"}
+_GATK = {"id": "gatk", "name": "GATK"}
+_MANTA = {"id": "manta", "name": "Manta"}
+_TIDDIT = {"id": "tiddit", "name": "TIDDIT"}
+
+CALLERS = {
+    "snv": [
+        {"id": "bcftools", "name": "Bcftools"},
+        {"id": "deepvariant", "name": "DeepVariant"},
+        _FREEBAYES,
+        _GATK,
+        {"id": "samtools", "name": "SAMtools"},
+    ],
+    "cancer": [
+        _FREEBAYES,
+        _GATK,
+        {"id": "mutect", "name": "MuTect"},
+        {"id": "pindel", "name": "Pindel"},
+        {"id": "tnscope", "name": "TNScope"},
+        {"id": "tnscope_umi", "name": "TNscope_UMI"},
+        {"id": "vardict", "name": "VarDict"},
+    ],
+    "cancer_sv": [
+        {"id": "ascat", "name": "ASCAT"},
+        {"id": "cnvkit", "name": "CNVkit"},
+        {"id": "dellysv", "name": "DellySV"},
+        {"id": "dellycnv", "name": "DellyCNV"},
+        _GATK,
+        {"id": "igh_dux4", "name": "IGH-DUX4 detection"},
+        _MANTA,
+        _TIDDIT,
+    ],
+    "mei": [{"id": "retroseq", "name": "RetroSeq"}],
+    "sv": [
+        {"id": "cnvnator", "name": "CNVnator"},
+        {"id": "cnvpytor", "name": "CNVpytor"},
+        {"id": "delly", "name": "Delly"},
+        _GATK,
+        {"id": "hificnv", "name": "HiFiCNV"},
+        _MANTA,
+        {"id": "severus", "name": "Severus"},
+        {"id": "sniffles", "name": "Sniffles"},
+        _TIDDIT,
+    ],
+    "str": [
+        {"id": "expansionhunter", "name": "ExpansionHunter"},
+        {"id": "trgt", "name": "TRGT"},
+    ],
+    "fusion": [
+        {"id": "arriba", "name": "Arriba"},
+        {"id": "fusioncatcher", "name": "FusionCatcher"},
+        {"id": "starfusion", "name": "STARfusion"},
+    ],
 }

scout/export/panel.py

@@ -1,7 +1,10 @@
 # -*- coding: utf-8 -*-
 import logging
+from typing import List
 
+from scout.adapter.mongo.base import MongoAdapter
 from scout.constants import CHROMOSOME_INTEGERS, CHROMOSOMES
+from scout.constants.panels import EXPORT_PANEL_FIELDS
 
 LOG = logging.getLogger(__name__)
 
@@ -14,7 +17,6 @@ def export_panels(adapter, panels, versions=None, build="37"):
     Args:
         adapter(scout.adapter.MongoAdapter)
         panels(iterable(str)): Iterable with panel ids
-        bed(bool): If lines should be bed formated
     """
     if versions and (len(versions) != len(panels)):
         raise SyntaxError("If version specify for each panel")
@@ -111,28 +113,30 @@ def export_panels(adapter, panels, versions=None, build="37"):
         yield gene_line
 
 
-def export_gene_panels(adapter, panels, version=None):
+def set_export_fields(panels: list[str]) -> list[tuple]:
+    """Set the field that should be exported for one panel or a list of panels."""
+
+    if len(panels) == 1:
+        return EXPORT_PANEL_FIELDS
+
+    # if more than one panel is exported (from the CLI) - export only HGNC and symbol
+    return EXPORT_PANEL_FIELDS[:2]
+
+
+def export_gene_panels(adapter: MongoAdapter, panels: List[str], version: float = None):
     """Export the genes of a gene panel
 
     Takes a list of gene panel names and return the lines of the gene panels.
     Unlike export_panels this function only export the genes and extra information,
     not the coordinates.
 
-    Args:
-        adapter(MongoAdapter)
-        panels(list(str))
-        version(float): Version number, only works when one panel
-
     Yields:
         gene panel lines
     """
+
     if version and len(panels) > 1:
         raise SyntaxError("Version only possible with one panel")
 
-    bed_string = "{0}\t{1}\t{2}\t{3}\t{4}\t{5}"
-
-    headers = []
-
     # Dictionary with hgnc ids as keys and panel gene information as value.
     panel_geneobjs = dict()
 
@@ -141,29 +145,22 @@ def export_gene_panels(adapter, panels, version=None):
         if not panel_obj:
             LOG.warning("Panel %s could not be found", panel_id)
             continue
+        panel_geneobjs.update({gene["hgnc_id"]: gene for gene in panel_obj.get("genes", [])})
 
-        for gene_obj in panel_obj["genes"]:
-            panel_geneobjs[gene_obj["hgnc_id"]] = gene_obj
-
-    if len(panel_geneobjs) == 0:
+    if not panel_geneobjs:
         return
 
-    headers.append(
-        "#hgnc_id\thgnc_symbol\tdisease_associated_transcripts\t"
-        "reduced_penetrance\tmosaicism\tdatabase_entry_version"
-    )
-
-    for header in headers:
-        yield header
+    header = []
+    header.append("\t".join(fields[0] for fields in EXPORT_PANEL_FIELDS))
+    yield from header
 
-    for hgnc_id in panel_geneobjs:
-        gene_obj = panel_geneobjs[hgnc_id]
-        gene_line = bed_string.format(
-            gene_obj["hgnc_id"],
-            gene_obj["symbol"],
-            ",".join(gene_obj.get("disease_associated_transcripts", [])),
-            gene_obj.get("reduced_penetrance", ""),
-            gene_obj.get("mosaicism", ""),
-            gene_obj.get("database_entry_version", ""),
-        )
-        yield gene_line
+    for gene_obj in panel_geneobjs.values():
+        gene_line_fields = [
+            (
+                ",".join(gene_obj.get(gene_key, ""))
+                if isinstance(gene_obj.get(gene_key), list)
+                else str(gene_obj.get(gene_key, ""))
+            )
+            for _, gene_key in set_export_fields(panels=panels)
+        ]
+        yield "\t".join(gene_line_fields)

scout/parse/panel.py

@@ -85,72 +85,63 @@ def get_hgnc_identifier(gene_info, id_type="hgnc_id"):
     return None
 
 
-def parse_gene(gene_info):
-    """Parse a gene line with information from a panel file
+def parse_gene(gene_info: dict) -> dict:
+    """Parse a gene line with information from a panel file."""
+
+    def get_alias_keys_value(alias_keys: list[str]) -> List[str]:
+        """Collect list of strings from the alias keys present in gene_info."""
+        return [
+            item.strip()
+            for alias_key in alias_keys
+            if alias_key in gene_info
+            for item in gene_info[alias_key].strip('"').split(",")
+            if item
+        ]
 
-    Args:
-        gene_info(dict): dictionary with gene info
-
-    Returns:
-        gene(dict): A dictionary with the gene information
-            {
-            'hgnc_id': int,
-            'hgnc_symbol': str,
-            'disease_associated_transcripts': list(str),
-            'inheritance_models': list(str),
-            'mosaicism': bool,
-            'reduced_penetrance': bool,
-            'database_entry_version': str,
-            }
-
-    """
     gene = {}
 
+    # Parse hgnc_id and handle errors
     hgnc_id = get_hgnc_identifier(gene_info, id_type="hgnc_id")
     if hgnc_id is not None:
         try:
             hgnc_id = int(hgnc_id)
         except ValueError:
-            raise SyntaxError("Invalid hgnc id: {0}".format(hgnc_id))
+            raise SyntaxError(f"Invalid hgnc id: {hgnc_id}")
 
     gene["hgnc_id"] = hgnc_id
-
     gene["hgnc_symbol"] = get_hgnc_identifier(gene_info, id_type="hgnc_symbol")
     gene["identifier"] = hgnc_id or gene["hgnc_symbol"]
 
-    # Disease associated transcripts is a ','-separated list of
-    # manually curated transcripts
-    transcripts = ""
-    for field in PANEL_GENE_INFO_TRANSCRIPTS:
-        if field not in gene_info:
-            continue
-        transcripts = gene_info[field].strip('"')
-
-    gene["transcripts"] = [
-        transcript.strip() for transcript in transcripts.split(",") if transcript
-    ]
-
-    # Genetic disease models is a ','-separated list of manually curated
-    # inheritance patterns that are followed for a gene
-    models = ""
-    for field in PANEL_GENE_INFO_MODELS:
-        if field not in gene_info:
-            continue
-        models = gene_info[field].strip().strip('"')
+    # Add list values from alias keys
+    gene.update(
+        {
+            "disease_associated_transcripts": get_alias_keys_value(PANEL_GENE_INFO_TRANSCRIPTS),
+            "inheritance_models": get_alias_keys_value(PANEL_GENE_INFO_MODELS),
+            "custom_inheritance_models": get_alias_keys_value(["custom_inheritance_models"]),
+        }
+    )
 
-    # Collect whichever model provided by the user.
-    # Then populate inheritance_models and custom_inheritance_models on gene build step
-    gene["inheritance_models"] = [model.strip() for model in models.split(",") if model != ""]
+    # Remove empty keys
+    gene = {k: v for k, v in gene.items() if v}
 
-    # If a gene is known to be associated with mosaicism this is annotated
-    gene["mosaicism"] = bool(gene_info.get("mosaicism"))
+    # Add boolean flags if they are True
+    gene.update(
+        {
+            key: True
+            for key in ["mosaicism", "reduced_penetrance"]
+            if gene_info.get(key) and gene_info.get(key) != ""
+        }
+    )
 
-    # If a gene is known to have reduced penetrance this is annotated
-    gene["reduced_penetrance"] = bool(gene_info.get("reduced_penetrance"))
+    # Add optional fields
+    gene.update(
+        {
+            key: gene_info[key]
+            for key in ["database_entry_version", "comment"]
+            if gene_info.get(key) and gene_info.get(key) != ""
+        }
+    )
 
-    # The database entry version is a way to track when a a gene was added or
-    # modified, optional
-    gene["database_entry_version"] = gene_info.get("database_entry_version")
     return gene
 
 
@@ -383,7 +374,7 @@ def parse_panel_app_panel(
     return gene_panel
 
 
-def get_omim_panel_genes(genemap2_lines, mim2gene_lines, alias_genes):
+def get_omim_panel_genes(genemap2_lines: list, mim2gene_lines: list, alias_genes: dict):
     """Return all genes that should be included in the OMIM-AUTO panel
     Return the hgnc symbols
 
@@ -424,6 +415,19 @@ def get_omim_panel_genes(genemap2_lines, mim2gene_lines, alias_genes):
                 break
 
         if hgnc_id_info:
-            yield {"hgnc_id": hgnc_id_info["true"], "hgnc_symbol": hgnc_symbol}
+            if hgnc_id_info["true"]:
+                hgnc_id = hgnc_id_info["true"]
+            elif len(hgnc_id_info.get("ids", ())) == 1:
+                hgnc_id = list(hgnc_id_info["ids"])[0]
+                LOG.warning(
+                    "Gene symbol %s does not exist: using an apparently unique alias for hgnc_id %s",
+                    hgnc_symbol,
+                    hgnc_id,
+                )
+            else:
+                LOG.warning(
+                    "Gene symbol %s does not exist, and as an alias it is not unique", hgnc_symbol
+                )
+            yield {"hgnc_id": hgnc_id, "hgnc_symbol": hgnc_symbol}
         else:
             LOG.warning("Gene symbol %s does not exist", hgnc_symbol)

scout/server/blueprints/alignviewers/views.py

@@ -127,6 +127,9 @@ def sashimi_igv(
 @alignviewers_bp.route(
     "/<institute_id>/<case_name>/<variant_id>/<chrom>/<start>/<stop>/igv", methods=["GET"]
 )  # from SV variant page, where you have to pass breakpoints coordinates
+@alignviewers_bp.route(
+    "/<institute_id>/<case_name>/<chrom>/<start>/<stop>/igv", methods=["GET"]
+)  # from SMN variant page
 def igv(
     institute_id: str,
     case_name: str,

scout/server/blueprints/cases/controllers.py

@@ -20,6 +20,7 @@ from scout.constants import (
     CASE_TAGS,
     CUSTOM_CASE_REPORTS,
     DATE_DAY_FORMATTER,
+    GENOME_REGION,
     INHERITANCE_PALETTE,
     MITODEL_HEADER,
     MT_COV_STATS_HEADER,
@@ -282,11 +283,14 @@ def sma_case(store, institute_obj, case_obj):
 
     _populate_case_individuals(case_obj)
 
+    case_has_alignments(case_obj)
+
     data = {
         "institute": institute_obj,
         "case": case_obj,
         "comments": store.events(institute_obj, case=case_obj, comments=True),
         "events": _get_events(store, institute_obj, case_obj),
+        "region": GENOME_REGION[case_obj.get("genome_build", "38")],
     }
     return data
 

scout/server/blueprints/cases/templates/cases/case_sma.html

@@ -50,7 +50,7 @@
           </div>
         </div> <!-- end of div class row -->
 
-        <div class="d-flex">
+        <span class="d-flex">
           {% if case.vcf_files.vcf_snv %}
           <span class="me-3">
             <form action="{{url_for('variants.variants', institute_id=institute._id, case_name=case.display_name) }}">
@@ -61,11 +61,19 @@
           </span>
           {% endif %}
           {% if case.vcf_files.vcf_sv %}
-          <form action="{{url_for('variants.sv_variants', institute_id=institute._id, case_name=case.display_name) }}">
-            <input type="hidden" id="hgnc_symbols" name="hgnc_symbols" value="SMN1, SMN2"></input>
-            <input type="hidden" id="gene_panels" name="gene_panels" value="['']"></input>
-            <button type="submit" class="btn btn-secondary btn-sm" target="_blank" rel="noopener" data-bs-toggle="tooltip" title="Structural variants view filtered for the genes SMN1 and SMN2">SVs</button></span>
-          </form>
+          <span class="me-3">
+            <form action="{{url_for('variants.sv_variants', institute_id=institute._id, case_name=case.display_name) }}">
+              <input type="hidden" id="hgnc_symbols" name="hgnc_symbols" value="SMN1, SMN2"></input>
+              <input type="hidden" id="gene_panels" name="gene_panels" value="['']"></input>
+              <button type="submit" class="btn btn-secondary btn-sm" target="_blank" rel="noopener" data-bs-toggle="tooltip" title="Structural variants view filtered for the genes SMN1 and SMN2">SVs</button></span>
+            </form>
+          </span>
+          {% endif %}
+          {% if case.bam_files %}
+            <span class="me-3"><a class="btn btn-secondary btn-sm text-white" href="{{url_for('alignviewers.igv', institute_id=case['owner'], case_name=case['display_name'], chrom=region['smn1']['chrom'], start=region['smn1']['start'], stop=region['smn1']['end'] )}}" target="_blank">IGV viewer SMN1</a></span>
+            <span class="me-3"><a class="btn btn-secondary btn-sm text-white" href="{{url_for('alignviewers.igv', institute_id=case['owner'], case_name=case['display_name'], chrom=region['smn2']['chrom'], start=region['smn2']['start'], stop=region['smn2']['end'] )}}" target="_blank">IGV viewer SMN2</a></span>
+          {% else %}
+            <span class="me-3 text-muted">BAM file(s) missing</span>
           {% endif %}
         </div>
 

scout/server/blueprints/cases/templates/cases/collapsible_actionbar.html

@@ -90,16 +90,24 @@
       <div href="#" class="bg-dark list-group-item text-white">
         <div class="d-flex flex-row flex-fill bd-highlight">
           <span class="menu-collapsed">Coverage (chanjo2)</span>
-          {{ chanjo2_report_form(institute, case, case.panel_names|join(', '), 'report', case.default_genes|join(','), "<span class='fa fa-link'></span>"|safe ) }} <!--chanjo2 report-->
+          {{ chanjo2_report_form(institute, case, case.panel_names|join(', '), 'report', case.default_genes|join(','), "<span class='fa fa-link' style='cursor: pointer;'></span>"|safe ) }} <!--chanjo2 report-->
         </div>
       </div>
+      {% if "38" in case.genome_build %}
+        <div href="#" class="bg-dark list-group-item text-white">
+          <div class="d-flex flex-row flex-fill bd-highlight">
+            <span class="menu-collapsed">MANE Coverage (chanjo2)</span>
+            {{ chanjo2_report_form(institute, case, case.panel_names|join(', '), 'mane_overview', case.default_genes|join(','), "<span class='fa fa-link' style='cursor: pointer;'></span>"|safe ) }} <!--chanjo2 MANE overview-->
+          </div>
+        </div>
+      {% endif %}
     {% endif %}
     {% if case.chanjo_coverage %}
       <div href="#" class="bg-dark list-group-item text-white">
         <div class="d-flex flex-row flex-fill bd-highlight">
           <span class="menu-collapsed">Coverage</span>
             <form method="POST" id="coverage_html" target="_blank" rel="noopener" action="{{ url_for('report.report', sample_id=case.individual_ids, level=institute.coverage_cutoff, panel_name=case.panel_names|join(', ')) }}">
-              <input type="hidden" name="gene_ids" value="{{ case.default_genes|join(',') }}"></input>
+              <input type="hidden" name="gene_ids" value="{{ case.default_genes|join(',') }}"/>
               <a href="javascript:;" onclick="document.getElementById('coverage_html').submit();">
                 <span class="fa fa-link"></span></a>
             </form>

scout/server/blueprints/cases/templates/cases/matchmaker.html

@@ -155,8 +155,13 @@
           <div class="card">
             <div class="card-header" id="heading_{{match_obj.match_oid}}">
               <h2 class="mb-0">
-                <button class="btn btn-link collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#div_{{match_obj.match_oid}}" aria-expanded="false" aria-controls="collapseTwo">
+                <button class="btn btn-link collapsed" type="button" {% if match_obj.patients|length == 0 %} disabled {% endif %} data-bs-toggle="collapse" data-bs-target="#div_{{match_obj.match_oid}}" aria-expanded="false" aria-controls="collapseTwo">
                   Match {{match_obj.match_date.strftime('%Y-%m-%d %H:%M')}}
+                  {% if match_obj.patients %}
+                    <span class="badge rounded-pill bg-success ms-3">matches: {{match_obj.patients|length}}</span>
+                  {% else %}
+                    <span class="badge rounded-pill bg-secondary ms-3">No matches available</span>
+                  {% endif %}
                 </button>
               </h2>
             </div>
@@ -177,14 +182,14 @@
                     {% for match_result in match_obj.patients %}
                        <tr class="{{ loop.cycle('odd', 'even') }}">
                          <td style="width: 5%" class="border-bottom-0"><span class="badge bg-primary rounded-pill">{{match_result.score.patient|round(4)}}</td>
-                         <td style="width: 10%">{{match_result.node.label}}</td>
-                         <td style="width: 15%">
+                         <td style="width: 10%" class="text-body"><strong>{{match_result.node.label}}</strong></td>
+                         <td style="width: 15%" class="text-body">
                            {% if "http" in match_result.patient_id %}
                             <a href="{{match_result.patient_id}}" target="_blank">link</a>
                            {% else %}
                             <strong>{{match_result.patient_id}}</strong></td>
                            {% endif %}
-                         <td style="width: 20%" class="text-break">
+                         <td style="width: 20%" class="text-break text-body">
                            {{match_result.patient.contact.name}}<br>
                            {% if "http" in match_result.patient.contact.href %}
                             <a href="{{match_result.patient.contact.href}}" target="_blank">contact link</a>
@@ -198,7 +203,7 @@
                              <br>{{match_result.patient.contact.email|replace("mailto:","")}}
                            {% endif %}
                          </td>
-                         <td style="width: 35%">
+                         <td style="width: 35%" class="text-body">
                            {% for feature in match_result.patient.features %}
                              <span data-bs-toggle="tooltip" title="{{feature.label or 'description not available'}}" class="badge bg-info">{{feature.label}}({{feature.id}})</span>
                            {% else %}
@@ -219,10 +224,10 @@
                        {% if match_result.patient.genomicFeatures%}
                          <tr class="{{ loop.cycle('odd', 'even') }}">
                            <td class="border-top-0"></td>
-                           <td style="width: 20%"><strong>Gene/Variants:</strong></td>
+                           <td style="width: 20%" class="text-body"><strong>Gene/Variants:</strong></td>
                            <td colspan="5">
                               {% for g_feat in match_result.patient.genomicFeatures %}
-                                <div style="display: flex;">
+                                <div style="display: flex;" class="text-body">
                                   <div style="margin-left: 20px;"><strong>{{loop.index}}</strong></div>
                                   <ul>
                                     <li><strong>{{ g_feat.gene._geneName}}</strong>

scout/server/blueprints/institutes/controllers.py

@@ -10,7 +10,13 @@ from pymongo.cursor import Cursor
 from werkzeug.datastructures import Headers, MultiDict
 
 from scout.adapter.mongo.base import MongoAdapter
-from scout.constants import CASE_STATUSES, DATE_DAY_FORMATTER, ID_PROJECTION, PHENOTYPE_GROUPS
+from scout.constants import (
+    CASE_STATUSES,
+    DATE_DAY_FORMATTER,
+    ID_PROJECTION,
+    PHENOTYPE_GROUPS,
+    VARIANTS_TARGET_FROM_CATEGORY,
+)
 from scout.server.blueprints.variant.utils import predictions, update_representative_gene
 from scout.server.extensions import beacon, store
 from scout.server.utils import institute_and_case, user_institutes
@@ -434,7 +440,7 @@ def cases(store, request, institute_id):
     data["institute"] = institute_obj
 
     name_query = request.form
-    limit = int(request.args.get("search_limit")) if request.args.get("search_limit") else 100
+    limit = int(request.form.get("search_limit")) if request.form.get("search_limit") else 100
 
     data["form"] = CaseFilterForm(request.form)
 
@@ -669,7 +675,7 @@ def export_gene_variants(
         variant_line.append(variant.get("display_name"))  # Position
         variant_line.append(str(variant.get("rank_score", "")))  # Score
         variant_genes = [
-            gene.get("hgnc_symbol", gene.get("hgnc_id")) for gene in variant.get("genes", [])
+            gene.get("hgnc_symbol", str(gene.get("hgnc_id"))) for gene in variant.get("genes", [])
         ]
         variant_line.append(" | ".join(variant_genes))  # Genes
 
@@ -736,7 +742,8 @@ def gene_variants(store, pymongo_cursor, variant_count, page=1, per_page=50):
 def filters(store, institute_id):
     """Retrieve all filters for an institute"""
     filters = []
-    categories = ["cancer", "snv", "str", "sv"]
+
+    categories = VARIANTS_TARGET_FROM_CATEGORY.keys()
     for category in categories:
         category_filters = store.filters(institute_id, category)
         filters.extend(category_filters)

scout/server/blueprints/institutes/templates/overview/causatives.html

@@ -29,7 +29,7 @@
 <div class="container-float">
   <div class="row" id="body-row"> <!--sidebar and main container are on the same row-->
     <div class="col-12">
-        {{ variant_list_content(institute, causatives, acmg_map, callers) }}
+        {{ variant_list_content(institute, causatives, acmg_map, callers, inherit_palette) }}
     </div>
   </div> <!-- end of div id body-row -->
 </div>

scout/server/blueprints/institutes/templates/overview/gene_variants.html

@@ -1,5 +1,5 @@
 {% extends "layout.html" %}
-{% from "variants/components.html" import frequency_cell_general, variant_funct_anno_cell, variant_gene_symbols_cell, variant_region_anno_cell %}
+{% from "variants/components.html" import frequency_cell_general, variant_funct_anno_cell, variant_gene_symbols_cell %}
 {% from "utils.html" import comments_table %}
 {% from "overview/institute_sidebar.html" import institute_actionbar %}
 {% from "variants/utils.html" import pagination_footer, pagination_hidden_div %}
@@ -43,7 +43,6 @@
           <th scope="col">Gene</th>
           <th scope="col">Pop Freq</th>
           <th scope="col">CADD</th>
-          <th scope="col">Region</th>
           <th scope="col">Function</th>
         </tr>
 </thead>
@@ -56,16 +55,15 @@
       {% endif %}
             <td class="align-middle">{{ cell_rank(variant) }}</td>
             <td class="align-middle">{{ pretty_link_no_gene(variant) }} </td>
-            <td class="align-middle">{{ variant_gene_symbols_cell(variant) }}</td>
+            <td class="align-middle">{{ variant_gene_symbols_cell(variant, inherit_palette) }}</td>
             <td class="align-middle">{{ frequency_cell_general(variant) }}</td>
             <td class="align-middle">{{ cell_cadd(variant) }}</td>
-            <td class="align-middle">{{ variant_region_anno_cell(variant) }}</td>
             <td class="align-middle">{{ variant_funct_anno_cell(variant) }}</td>
           </tr>
         {% endfor %}
         {% if form.hgnc_symbols.data == [] %}
         <tr>
-          <td colspan=7>
+          <td colspan=6>
             No variants to display
           </td>
         </tr>

scout/server/blueprints/institutes/templates/overview/utils.html

@@ -311,7 +311,7 @@
 {% endmacro %}
 
 
-{% macro variant_list_content(institute, variants, acmg_map, callers) %}
+{% macro variant_list_content(institute, variants, acmg_map, callers, inherit_palette) %}
 <div class="card mt-3">
   <div class="card-body overflow-auto">
     <table id="variants_table" class="table display table-sm">
@@ -348,7 +348,7 @@
               {% if variant.category == "fusion" %}
                 {{ fusion_variant_gene_symbols_cell(variant) }}
               {% else %}
-                {{ variant_gene_symbols_cell(variant) }}
+                {{ variant_gene_symbols_cell(variant, inherit_palette) }}
               {% endif %}
             </td>
             <td><!-- Variant link -->

scout/server/blueprints/institutes/templates/overview/verified.html

@@ -58,7 +58,7 @@
         {{validated_chart()}}
       </div>
       <div class="row">
-        <div class="col-12">{{ variant_list_content(institute, verified, acmg_map, callers) }}</div>
+        <div class="col-12">{{ variant_list_content(institute, verified, acmg_map, callers, inherit_palette) }}</div>
       </div>
     </div>
   </div>

scout/server/blueprints/institutes/views.py

@@ -6,7 +6,14 @@ from flask import Blueprint, flash, jsonify, redirect, render_template, request
 from flask_login import current_user
 from pymongo import DESCENDING
 
-from scout.constants import ACMG_COMPLETE_MAP, ACMG_MAP, CALLERS, VERBS_ICONS_MAP, VERBS_MAP
+from scout.constants import (
+    ACMG_COMPLETE_MAP,
+    ACMG_MAP,
+    CALLERS,
+    INHERITANCE_PALETTE,
+    VERBS_ICONS_MAP,
+    VERBS_MAP,
+)
 from scout.server.blueprints.variants.controllers import update_form_hgnc_symbols
 from scout.server.extensions import beacon, loqusdb, store
 from scout.server.utils import institute_and_case, jsonconverter, templated, user_institutes
@@ -63,11 +70,12 @@ def verified(institute_id):
     verified_vars = controllers.verified_vars(institute_id)
     verified_stats = controllers.verified_stats(institute_id, verified_vars)
     return dict(
+        acmg_map={key: ACMG_COMPLETE_MAP[value] for key, value in ACMG_MAP.items()},
+        callers=CALLERS,
+        inherit_palette=INHERITANCE_PALETTE,
         institute=institute_obj,
         verified=verified_vars,
         verified_stats=verified_stats,
-        acmg_map={key: ACMG_COMPLETE_MAP[value] for key, value in ACMG_MAP.items()},
-        callers=CALLERS,
     )
 
 
@@ -76,10 +84,11 @@ def verified(institute_id):
 def causatives(institute_id):
     institute_obj = institute_and_case(store, institute_id)
     return dict(
-        institute=institute_obj,
-        causatives=controllers.causatives(institute_obj, request),
         acmg_map={key: ACMG_COMPLETE_MAP[value] for key, value in ACMG_MAP.items()},
         callers=CALLERS,
+        causatives=controllers.causatives(institute_obj, request),
+        institute=institute_obj,
+        inherit_palette=INHERITANCE_PALETTE,
     )
 
 
@@ -168,7 +177,14 @@ def gene_variants(institute_id):
             store, results, result_size, page
         )  # decorated variant results, max 50 in a page
 
-    return dict(institute=institute_obj, form=form, page=page, result_size=result_size, **data)
+    return dict(
+        institute=institute_obj,
+        form=form,
+        inherit_palette=INHERITANCE_PALETTE,
+        page=page,
+        result_size=result_size,
+        **data,
+    )
 
 
 # MOST OF THE CONTENT OF THIS ENDPOINT WILL BE REMOVED AND INCLUDED INTO THE BEACON EXTENSION UNDER SERVER/EXTENSIONS