scout-browser 4.95.0__py3-none-any.whl → 4.97.0__py3-none-any.whl

scout/server/blueprints/institutes/forms.py

@@ -95,7 +95,11 @@ class InstituteForm(FlaskForm):
 
     alamut_institution = StringField("Alamut Institution ID", validators=[validators.Optional()])
 
-    check_show_all_vars = BooleanField("Preselect 'Show also variants only present in unaffected'")
+    check_show_all_vars = BooleanField("Preselect 'Include variants only present in unaffected'")
+
+    soft_filters = NonValidatingSelectMultipleField(
+        "Default soft filters", validators=[validators.Optional()]
+    )
 
     clinvar_key = StringField("API key", widget=PasswordInput(hide_value=False))
 

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

@@ -104,6 +104,13 @@
       placeholder: "Add Sanger email",
     });
 
+    $('#soft_filters').select2({
+      tags: true,
+      theme: 'bootstrap-5',
+      tokenSeparators: [','],
+      placeholder: "germline_risk",
+    });
+
     $('#clinvar_tags').select2({
       tags: true,
       theme: 'bootstrap-5',

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

@@ -285,7 +285,7 @@
             </div>
             <!-- End of cohorts settings -->
 
-            <!-- Variants and panels searching -->
+             <!-- Variants and panels searching -->
             <div class="row mt-5 d-flex align-items-center">
             <fieldset>
               <legend>Variants and gene panels searching</legend>
@@ -349,6 +349,25 @@
               </div>
               <!-- End of loqusdb settings -->
 
+              <!-- Custom soft filters for variants -->
+              <div class="row mt-5 d-flex align-items-center">
+                <fieldset>
+                  <legend>Variants custom soft filters</legend>
+                  <div class="row">
+                    <div class="col-sm-6 col-lg-4">
+                      {{form.soft_filters.label(class="control-label", data_bs_toggle="tooltip", data_bs_placement="top", title="Values to filter variant documents with by default. For example germline_risk or in_normal.")}}
+                      <select class="select2" id="soft_filters" name="soft_filters" multiple="true" style="width:100%;">
+                        {% if institute.soft_filters %}
+                          {% for filter in institute.soft_filters %}
+                            <option value="{{filter}}" selected>{{filter}}</option>
+                          {% endfor %}
+                        {% endif %}
+                      </select>
+                    </div>
+                  </div>
+              </div>
+              <!-- End of custom soft filters for variants -->
+
               <!-- Alamut settings -->
               <div class="row mt-5 d-flex align-items-center">
                 <fieldset><legend>Alamut Plus<a class="ms-2 text-decoration-none" href="https://extranet.interactive-biosoftware.com/alamut-visual-plus_API.html" target="_blank" rel="noopener">*</a></legend>

scout/server/blueprints/omics_variants/templates/omics_variants/outliers.html

@@ -59,7 +59,7 @@
               <tr>
                 <th style="width:14%" title="HGNC symbols">Gene</th>
                 <th style="width:7%" title="Sub-category">Type</th>
-                <th style="width:7%" title="Value - delta Psi or l2fc ">Value</th>
+                <th style="width:7%" title="Value - delta Psi or l2fc">Value</th>
                 <th title="Functional annotation">Func. annotation</th>
                 <th style="width:7%" title="P-value">P-value</th>
                 <th style="width:10%" title="Individual">Ind</th>
@@ -246,6 +246,13 @@
   <div class="col-6">
     {{ stash_filter_buttons(form, institute, case) }}
   </div>
+
+  <div class="col-2 offset-2">
+      <div class="btn-group">
+        {{ form.sort_by(class="form-select btn btn-primary", style="width: auto;") }}
+        {{ form.sort_order(class="form-select btn btn-primary", style="width: auto;") }}
+      </div>
+    </div>
 </div>
 {% endmacro %}
 
@@ -266,7 +273,7 @@
     <div class="col-4 d-flex justify-content-center">
       Filter returns {{result_size}} / {{ total_variants }} variants.
     </div>
-    <div class="col-4 d-flex flex-column justify-content-end">
+    <div class="col-4 d-flex justify-content-end">
       <div class="d-flex justify-content-end">Showing {%if more_variants %}page {{page}}{%else%}last page{% endif %} with {{nvars}} variants.</div>
     </div>
   </div>

scout/server/blueprints/omics_variants/views.py

@@ -11,6 +11,9 @@ from scout.server.blueprints.variants.controllers import (
     get_variants_page,
     populate_chrom_choices,
     populate_filters_form,
+    populate_persistent_filters_choices,
+    set_hpo_clinical_filter,
+    update_form_hgnc_symbols,
 )
 from scout.server.blueprints.variants.forms import OutlierFiltersForm
 from scout.server.extensions import store
@@ -43,8 +46,7 @@ def outliers(institute_id, case_name):
         variant_type = "clinical"
     variants_stats = store.case_variants_count(case_obj["_id"], institute_id, variant_type, False)
 
-    if request.form.get("hpo_clinical_filter"):
-        case_obj["hpo_clinical_filter"] = True
+    set_hpo_clinical_filter(case_obj, request.form)
 
     # update status of case if visited for the first time
     activate_case(store, institute_obj, case_obj, current_user)
@@ -63,12 +65,6 @@ def outliers(institute_id, case_name):
             store, institute_obj, case_obj, user_obj, category, request.form
         )
 
-    # populate filters dropdown
-    available_filters = list(store.filters(institute_obj["_id"], category))
-    form.filters.choices = [
-        (filter.get("_id"), filter.get("display_name")) for filter in available_filters
-    ]
-
     # populate available panel choices
     form.gene_panels.choices = gene_panel_choices(store, institute_obj, case_obj)
 
@@ -78,7 +74,7 @@ def outliers(institute_id, case_name):
     genome_build = "38" if "38" in str(case_obj.get("genome_build", "37")) else "37"
     cytobands = store.cytoband_by_chrom(genome_build)
 
-    # controllers.update_form_hgnc_symbols(store, case_obj, form)
+    update_form_hgnc_symbols(store, case_obj, form)
     variants_query = store.omics_variants(
         case_obj["_id"], query=form.data, category=category, build=genome_build
     )
@@ -96,7 +92,9 @@ def outliers(institute_id, case_name):
         case=case_obj,
         cytobands=cytobands,
         expand_search=get_expand_search(request.form),
-        filters=available_filters,
+        filters=populate_persistent_filters_choices(
+            institute_id=institute_id, category=category, form=form
+        ),
         form=form,
         inherit_palette=INHERITANCE_PALETTE,
         institute=institute_obj,

scout/server/blueprints/variant/controllers.py

@@ -32,10 +32,12 @@ from scout.server.blueprints.variant.utils import (
     update_variant_case_panels,
 )
 from scout.server.blueprints.variants.utils import update_case_panels
-from scout.server.extensions import LoqusDB, config_igv_tracks, gens
+from scout.server.extensions import LoqusDB, chanjo2, config_igv_tracks, gens
 from scout.server.links import disease_link, get_variant_links
 from scout.server.utils import (
     case_has_alignments,
+    case_has_chanjo2_coverage,
+    case_has_chanjo_coverage,
     case_has_mt_alignments,
     case_has_rna_tracks,
     user_institutes,
@@ -257,6 +259,8 @@ def variant(
     # Provide basic info on alignment files availability for this case
     case_has_alignments(case_obj)
     case_has_mt_alignments(case_obj)
+    case_has_chanjo_coverage(case_obj)
+    case_has_chanjo2_coverage(case_obj)
 
     # Collect all the events for the variant
     events = list(store.events(institute_obj, case=case_obj, variant_id=variant_id))
@@ -402,6 +406,9 @@ def variant(
         "inherit_palette": INHERITANCE_PALETTE,
         "igv_tracks": get_igv_tracks("38" if variant_obj["is_mitochondrial"] else genome_build),
         "has_rna_tracks": case_has_rna_tracks(case_obj),
+        "gene_has_full_coverage": get_gene_has_full_coverage(
+            institute_obj, case_obj, variant_obj, genome_build
+        ),
         "gens_info": gens.connection_settings(genome_build),
         "evaluations": evaluations,
         "ccv_evaluations": ccv_evaluations,
@@ -409,6 +416,28 @@ def variant(
     }
 
 
+def get_gene_has_full_coverage(
+    institute_obj, case_obj, variant_obj, genome_build
+) -> Dict[int, bool]:
+    """
+    Query chanjo2, if configured and d4 files are available for this case,
+    for coverage completeness on the genes touching this variant.
+    """
+    if not case_obj.get("chanjo2_coverage"):
+        return {}
+
+    gene_has_full_coverage: dict = {
+        hgnc_id: chanjo2.get_gene_complete_coverage(
+            hgnc_id=hgnc_id,
+            threshold=institute_obj.get("coverage_cutoff") or 15,
+            individuals=case_obj.get("individuals"),
+            build=genome_build,
+        )
+        for hgnc_id in [gene.get("hgnc_id") for gene in variant_obj.get("genes")]
+    }
+    return gene_has_full_coverage
+
+
 def variant_rank_scores(store: MongoAdapter, case_obj: dict, variant_obj: dict) -> list:
     """Retrive rank score values and ranges for the variant
 

scout/server/blueprints/variant/templates/variant/cancer-variant.html

@@ -223,9 +223,25 @@
       {% if tmp_gene_info %}
         {% set primary_transcript = tmp_gene_info[1] %}
         {% set nr_genes = variant.genes | length %}
-        <a target="_blank" href="{{ url_for('genes.gene', hgnc_id=primary_gene.hgnc_id) }}" data-bs-toggle="tooltip" title="Preferred gene for variant {% if nr_genes > 1 %} out of {{ nr_genes }} {% endif %}- shows conceptually highest impact change. See Severity card and Transcripts table below for more details."><h5 class="card-title">
-          {{ primary_gene.hgnc_symbol }}; {{ primary_gene.description }} {% if nr_genes > 1 %} <span class="badge bg-info">+ {{ nr_genes-1 }} genes</span>{% endif %}
-        </h5></a>
+        <table class="table table-bordered table-fixed table-sm">
+          <thead class="thead table-light border-top">
+            <tr class="active">
+              <th>Gene</th>
+              <th>Description</th>
+              <th data-bs-toggle="tooltip" title="Gene tolerance to a single copy of a truncating mutation (pLI) | Loss-of-function observed/expected upper bound fraction (LOEUF)">pLI score|LOEUF</th>
+            </tr>
+          </thead>
+          <tbody>
+            <tr>
+              <td>
+                <a target="_blank" href="{{ url_for('genes.gene', hgnc_id=primary_gene.hgnc_id) }}" data-bs-toggle="tooltip" title="Preferred gene for variant {% if nr_genes > 1 %} out of {{ nr_genes }} {% endif %}- shows conceptually highest impact change. See Severity card and Transcripts table below for more details.">{{ primary_gene.hgnc_symbol }}</a>
+                {% if nr_genes > 1 %} <span class="badge bg-info">+ {{ nr_genes-1 }} genes</span>{% endif %}
+              </td>
+              <td>{{primary_gene.description}}</td>
+              <td>{{primary_gene.pli_score|round(2) if primary_gene.pli_score else "n.a."}} | {{primary_gene.loeuf|round(2) if primary_gene.loeuf else "n.a."}}</td>
+            </tr>
+          </tbody>
+        </table>
       {% endif %}
       <ul class="list-group list-group-flush" style="margin-bottom: 1rem">
         {% if primary_transcript %}
@@ -235,10 +251,10 @@
           <span class="text-muted">exon </span><strong>{{ primary_gene.exon }}</strong>
         {% endif %}
         {% if primary_transcript and primary_transcript.coding_sequence_name %}
-              {{ primary_transcript.coding_sequence_name | url_decode }}
+              {{ primary_transcript.coding_sequence_name | url_decode | truncate(50, True) }}
         {% endif %}
         {% if primary_transcript and primary_transcript.protein_sequence_name %}
-          <strong>{{ primary_transcript.protein_sequence_name | url_decode }}</strong>
+          <strong>{{ primary_transcript.protein_sequence_name | url_decode | truncate(50, True) }}</strong>
         {% endif %}
         {% if primary_gene and primary_gene.region_annotation %}
           <div>(<span class="font-weight-bold">{{ primary_gene.functional_annotation|truncate(20, True) }}</span> in <span class="font-weight-bold">{{ primary_gene.region_annotation }} region</span>)</div>

scout/server/blueprints/variant/templates/variant/components.html

@@ -1,3 +1,4 @@
+{% from "cases/chanjo2_form.html" import chanjo2_report_form %}
 {% from "variant/buttons.html" import variant_tag_button, variant_tier_button, dismiss_variant_button, mosaic_variant_button %}
 {% from "variants/utils.html" import compounds_table %}
 {% from "variant/variant_details.html" import severity_list %}
@@ -118,15 +119,7 @@
         {% endif %}
         </div>
       {% endfor %}
-      {% if config.chanjo_report %}
-        <div class="d-flex flex-wrap ms-1">
-          {% for gene in variant.genes %}
-            <a class="btn btn-sm btn-secondary text-white" rel="noopener noreferrer" target="_blank" href="{{ url_for('report.gene', gene_id=gene.hgnc_id, sample_id=variant.samples|map(attribute='sample_id')|list) }}">
-              Gene coverage: {{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }}
-            </a>
-          {% endfor %}
-        </div>
-      {% endif %}
+      {{ gene_coverage(institute, variant, case, config) }}
     </li>
     <li class="list-group-item">
       <div>
@@ -136,6 +129,30 @@
   </ul>
 {% endmacro %}
 
+{% macro gene_coverage(institute, variant, case, config) %}
+  {% if case.chanjo_coverage and config.chanjo_report %}
+    <div class="d-flex flex-wrap ms-1">
+      {% for gene in variant.genes %}
+        <a class="btn btn-sm btn-secondary text-white" rel="noopener noreferrer" target="_blank" href="{{ url_for('report.gene', gene_id=gene.hgnc_id, sample_id=variant.samples|map(attribute='sample_id')|list) }}" data-bs-toggle="tooltip" title="Chanjo coverage report">
+          Gene coverage: {{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }}
+        </a>
+      {% endfor %}
+    </div>
+  {% endif %}
+  {% if case.chanjo2_coverage %}
+    <div class="d-flex flex-wrap ms-1" data-bs-toggle="tooltip" title="Chanjo2 coverage reports">
+      {% for gene in variant.genes %}
+        {{ chanjo2_report_form(institute, case, gene.hgnc_symbol, 'overview', gene.hgnc_id, "Gene coverage " + (gene.common.hgnc_symbol if gene.common else gene.hgnc_id), "btn btn-sm btn-secondary text-white") }} <!--chanjo2 genes overview -->
+        {% if gene.common.hgnc_id in gene_has_full_coverage and gene.common.hgnc_id[gene.common.hgnc_id] %}
+          <span class="bg-success fa-solid fa-circle-check" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Chanjo2 coverage is at 100% completeness."></span>
+        {% else %}
+          <span class="bg-warning fa-solid fa-triangle-exclamation" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Note that Chanjo2 coverage is below 100% completeness."></span>
+        {% endif %}
+      {% endfor %}
+    </div>
+  {% endif %}
+{% endmacro %}
+
 {% macro acmg_form(institute, case, variant, ACMG_OPTIONS, selected=None) %}
   <form action="{{ url_for('variant.variant_update', institute_id=institute._id, case_name=case.display_name, variant_id=variant._id) }}" method="POST">
     <div class="d-flex justify-content-between">

scout/server/blueprints/variant/templates/variant/variant.html

@@ -339,6 +339,7 @@
         <thead class="thead table-light border-top">
           <tr class="active">
             <th>Gene</th>
+            <th data-bs-toggle="tooltip" title="Gene tolerance to a single copy of a truncating mutation (pLI) | Loss-of-function observed/expected upper bound fraction (LOEUF)">pLI score|LOEUF</th>
             <th>Region</th>
             <th>Consequence</th>
             {% if case.genome_build == "38" %}
@@ -349,11 +350,12 @@
         <tbody>
           {% for gene in variant.genes %}
             <tr>
-              <th>
+              <td>
                 <a href="{{ url_for('genes.gene', hgnc_id=gene.hgnc_id) }}">
                   {{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }}
                 </a>
-              </th>
+              </td>
+              <td>{{gene.pli_score|round(2) if gene.pli_score else "n.a."}} | {{gene.loeuf|round(2) if gene.loeuf else "n.a."}}</td>
               <td>{{ gene.region_annotation }}</td>
               <td>{{ gene.functional_annotation|truncate(20, True) }}</td>
               {% if case.genome_build == "38" %} <!-- Display eventual functional annotations associated to MANE transcripts -->

scout/server/blueprints/variant/templates/variant/variant_details.html

@@ -375,7 +375,7 @@
         </li>
         <li class="list-group-item">
           SPIDEX
-          <span class="float-end">{{ variant.spidex_human }}</span>
+          <span class="float-end">{{ variant.spidex|spidex_human if variant.spidex else none|spidex_human }}</span>
         </li>
         <li class="list-group-item">
           <a href="{{ variant.spliceai_link }}" target="_blank" rel="noopener">SpliceAI</a> <a href="https://github.com/Illumina/SpliceAI" target="_blank" rel="noopener">DS max</a>

scout/server/blueprints/variant/utils.py

@@ -282,6 +282,8 @@ def add_gene_info(
             )
 
             all_models.update(set(variant_gene["manual_inheritance"]))
+            variant_gene["pli_score"] = hgnc_gene.get("pli_score")
+            variant_gene["loeuf"] = hgnc_gene.get("constraint_lof_oe_ci_upper")
 
             update_inheritance_model(variant_gene, all_models, disease_terms)
 

scout/server/blueprints/variant/views.py

@@ -27,12 +27,19 @@ from scout.server.blueprints.variant.controllers import (
     check_reset_variant_classification,
 )
 from scout.server.blueprints.variant.controllers import evaluation as evaluation_controller
-from scout.server.blueprints.variant.controllers import observations, str_variant_reviewer
+from scout.server.blueprints.variant.controllers import (
+    observations,
+    str_variant_reviewer,
+)
 from scout.server.blueprints.variant.controllers import variant as variant_controller
 from scout.server.blueprints.variant.controllers import variant_acmg as acmg_controller
-from scout.server.blueprints.variant.controllers import variant_acmg_post
+from scout.server.blueprints.variant.controllers import (
+    variant_acmg_post,
+)
 from scout.server.blueprints.variant.controllers import variant_ccv as ccv_controller
-from scout.server.blueprints.variant.controllers import variant_ccv_post
+from scout.server.blueprints.variant.controllers import (
+    variant_ccv_post,
+)
 from scout.server.blueprints.variant.verification_controllers import (
     MissingVerificationRecipientError,
     variant_verification,

scout/server/blueprints/variants/controllers.py

@@ -40,6 +40,7 @@ from scout.server.blueprints.variant.utils import (
     update_variant_case_panels,
 )
 from scout.server.blueprints.variants.forms import BetterDecimalField
+from scout.server.extensions import store
 from scout.server.links import add_gene_links, cosmic_links, str_source_link
 from scout.server.utils import (
     case_has_alignments,
@@ -83,6 +84,20 @@ def populate_force_show_unaffected_vars(institute_obj, form):
         form.show_unaffected.data = True
 
 
+def populate_persistent_filters_choices(
+    institute_id: str, category: str, form: ImmutableMultiDict
+) -> List[dict]:
+    """Populate the options present in the form.filters on variants page, directly setting on the form.
+    Also return a convenient list of filters for use in filter update macros.
+    """
+    available_filters = list(store.filters(institute_id, category))
+    form.filters.choices = [
+        (filter.get("_id"), filter.get("display_name"))
+        for filter in sorted(available_filters, key=lambda f: f.get("display_name", "").lower())
+    ]
+    return available_filters
+
+
 def populate_chrom_choices(form, case_obj):
     """Populate the option of the chromosome select according to the case genome build"""
     # Populate chromosome choices
@@ -90,6 +105,12 @@ def populate_chrom_choices(form, case_obj):
     form.chrom.choices = [(chrom, chrom) for chrom in chromosomes]
 
 
+def populate_institute_soft_filters(form, institute_obj):
+    """Populate the hidden field 'institute_soft_filters' with a string containing all institute's soft filters."""
+    if institute_obj.get("soft_filters"):
+        form.institute_soft_filters.data = ",".join(institute_obj["soft_filters"])
+
+
 def variants(
     store,
     institute_obj,
@@ -711,7 +732,7 @@ def _compound_follow_filter_clnsig(compound, compound_var_obj, query_form):
 
     There are some filter options that are rather unique, like the ClinVar one.
 
-    If clinsig_confident_always_returned is checked, variants are currently never dismissed on ClinSig alone.
+    If prioritise_clinvar is checked, variants are currently never dismissed on ClinSig alone.
 
     Args:
         compound(dict)
@@ -722,8 +743,7 @@ def _compound_follow_filter_clnsig(compound, compound_var_obj, query_form):
     query_rank = []
     query_str_rank = []
 
-    clinsig_always_returned = query_form.get("clinsig_confident_always_returned")
-    if clinsig_always_returned:
+    if query_form.get("prioritise_clinvar"):
         return False
 
     clinsig = query_form.get("clinsig")
@@ -2088,3 +2108,9 @@ def get_show_dismiss_block():
         session["show_dismiss_block"] = show_dismiss_block
 
     return show_dismiss_block
+
+
+def set_hpo_clinical_filter(case_obj: dict, request_form: dict):
+    """Set HPO clinical filter on case if requested through the form."""
+    if request_form.get("hpo_clinical_filter"):
+        case_obj["hpo_clinical_filter"] = True

scout/server/blueprints/variants/forms.py

@@ -113,6 +113,8 @@ class VariantFiltersForm(FlaskForm):
     compound_follow_filter = BooleanField("Compounds follow filter")
     cadd_inclusive = BooleanField("CADD inclusive")
     clinsig = NonValidatingSelectMultipleField("ClinVar CLINSIG", choices=CLINSIG_OPTIONS)
+    clinsig_exclude = BooleanField("Exclude")
+    prioritise_clinvar = BooleanField("Prioritise ClinVar")
 
     gnomad_frequency = BetterDecimalField("gnomadAF", validators=[validators.Optional()])
     local_obs_old = IntegerField("Local obs. (archive)", validators=[validators.Optional()])
@@ -151,11 +153,25 @@ class VariantFiltersForm(FlaskForm):
     cytoband_start = NonValidatingSelectField("Cytoband start", choices=[])
     cytoband_end = NonValidatingSelectField("Cytoband end", choices=[])
 
+    size_selector = NonValidatingSelectField(
+        "Variant size in bp", choices=[("$gte", ">="), ("$lt", "<")]
+    )
+    size = IntegerField(
+        "",
+        [
+            validators.Optional(),
+            validators.NumberRange(min=0, message="Number of bases must be 1 or greater."),
+        ],
+        widget=NumberInput(min=1),
+    )
+
     hide_dismissed = BooleanField("Hide dismissed", default=False)
     filter_variants = SubmitField(label="Filter variants")
     export = SubmitField(label="Filter and export")
 
-    show_unaffected = BooleanField("Show also variants present only in unaffected", default=False)
+    show_unaffected = BooleanField("Include variants present only in unaffected", default=True)
+    show_soft_filtered = BooleanField(f"Include soft-filtered variants", default=False)
+    institute_soft_filters = HiddenField()
 
 
 class FiltersForm(VariantFiltersForm):
@@ -163,11 +179,11 @@ class FiltersForm(VariantFiltersForm):
 
     symbol_file = FileField("Symbol File")
 
-    clinsig_confident_always_returned = BooleanField("CLINSIG Confident")
+    clinvar_trusted_revstat = BooleanField("CLINSIG Confident")
     spidex_human = SelectMultipleField("SPIDEX", choices=SPIDEX_CHOICES)
 
     clinical_filter = SubmitField(label="Clinical filter")
-    clinvar_tag = BooleanField("ClinVar hits")
+    clinvar_tag = BooleanField("ClinVar hits only")
 
     # polymorphic constant base for clinical filter
     clinical_filter_base = CLINICAL_FILTER_BASE
@@ -180,7 +196,7 @@ class CancerFiltersForm(VariantFiltersForm):
     alt_count = IntegerField("Min alt count", validators=[validators.Optional()])
     control_frequency = BetterDecimalField("Normal alt AF <", validators=[validators.Optional()])
     tumor_frequency = BetterDecimalField("Tumor alt AF >", validators=[validators.Optional()])
-    clinvar_tag = BooleanField("ClinVar hits")
+    clinvar_tag = BooleanField("ClinVar hits only")
     cosmic_tag = BooleanField("Cosmic hits")
     mvl_tag = BooleanField("Managed Variants hits")
     local_obs_cancer_somatic_old = IntegerField(
@@ -189,7 +205,6 @@ class CancerFiltersForm(VariantFiltersForm):
     local_obs_cancer_germline_old = IntegerField(
         "Local germline obs. (archive)", validators=[validators.Optional()]
     )
-
     # polymorphic constant base for clinical filter
     clinical_filter_base = CLINICAL_FILTER_BASE_CANCER
 
@@ -212,8 +227,6 @@ class StrFiltersForm(VariantFiltersForm):
 class SvFiltersForm(VariantFiltersForm):
     """Extends FiltersForm for structural variants"""
 
-    size = StringField("Length")
-    size_shorter = BooleanField("Length shorter than")
     svtype = SelectMultipleField("SVType", choices=SV_TYPE_CHOICES)
     decipher = BooleanField("Decipher")
     clingen_ngi = IntegerField("ClinGen NGI obs")
@@ -242,8 +255,6 @@ class CancerSvFiltersForm(SvFiltersForm):
 class FusionFiltersForm(VariantFiltersForm):
     """Extends FiltersForm for fusion variants"""
 
-    size = StringField("Length")
-    size_shorter = BooleanField("Length shorter than")
     decipher = BooleanField("Decipher")
     clinical_filter = SubmitField(label="Clinical filter")
     fusion_score = BetterDecimalField("Fusion score >=", validators=[validators.Optional()])
@@ -302,7 +313,23 @@ class OutlierFiltersForm(FlaskForm):
 
     clinical_filter_base = CLINICAL_FILTER_BASE_OUTLIER
 
-    show_unaffected = BooleanField("Show also variants present only in unaffected", default=False)
+    show_unaffected = BooleanField("Include variants present only in unaffected", default=False)
+
+    sort_by = NonValidatingSelectField(
+        choices=[
+            ("", "Sort by"),
+            ("p_value", "Sort by P-value"),
+            ("delta_psi", "Sort by Δψ"),
+            ("psi_value", "Sort by ψ value"),
+            ("zscore", "Sort by zscore"),
+            ("l2fc", "Sort by l2fc"),
+        ],
+        validators=[validators.Optional()],
+    )
+    sort_order = NonValidatingSelectField(
+        choices=[("", "Sort order"), ("asc", "asc"), ("desc", "desc")],
+        validators=[validators.Optional()],
+    )
 
 
 FILTERSFORMCLASS = {

scout/server/blueprints/variants/templates/variants/cancer-variants.html

@@ -83,17 +83,18 @@
             </td>
             <td>{{ gene_cell(variant) }}</td>
             <td>
+
               <a target="_blank" href="{{ url_for('variant.cancer_variant', institute_id=institute._id, case_name=case.display_name,
                                   variant_id=variant._id, cancer='yes') }}">
                 {% if variant.first_rep_gene.hgvs_identifier %}
-                  <div>{{ variant.first_rep_gene.hgvs_identifier }}</div>
-                  <div>{{ (variant.first_rep_gene.hgvsp_identifier or '') |url_decode }}</div>
+                  <div>{{ variant.first_rep_gene.hgvs_identifier|truncate(30, True) }}</div>
+                  <div>{{ (variant.first_rep_gene.hgvsp_identifier or '') |url_decode|truncate(30, True) }}</div>
                 {% else %}
-                  <div>{{ variant.reference }}→
+                  <div>{{ variant.reference|truncate(30, True) }}→
                     {% if variant.alternative | length > 5 %}
                       {{ variant.alternative[0] }}...{{ variant.alternative[-1] }}
                     {% else %}
-                      {{ variant.alternative }}
+                      {{ variant.alternative|truncate(30, True) }}
                     {% endif %}
                   </div>
                 {% endif %}

scout/server/blueprints/variants/templates/variants/components.html

@@ -203,16 +203,18 @@
       {% endfor %}
 
       {% set panel_count = matching_panels|length %}
-      <a
-        class="badge bg-secondary text-white"
-        data-bs-toggle="popover"
-        data-bs-html="true"
-        data-bs-trigger="hover click"
-        title="Overlapping gene panels"
-        data-bs-content="{% for panel in matching_panels %}
-          {{ panel.panel_name|safe }}<br>
-        {% else %} No ovelapping gene panels {% endfor %}"
-      >{{ panel_count }}</a>
+      {% if panel_count %}
+        <a
+          class="badge bg-secondary text-white"
+          data-bs-toggle="popover"
+          data-bs-html="true"
+          data-bs-trigger="hover click"
+          title="Overlapping gene panels"
+          data-bs-content="{% for panel in matching_panels %}
+            {{ panel.panel_name|safe }}<br>
+          {% endfor %}"
+        >{{ panel_count }}</a>
+      {% endif %}
     {% endmacro %}
 
     {% if variant.category in ["cancer", "sv_cancer"] %}