scout-browser 4.90.1__py3-none-any.whl → 4.91__py3-none-any.whl

scout/load/panelapp.py

@@ -0,0 +1,138 @@
+import logging
+import math
+from datetime import datetime
+from typing import Dict, List, Set
+
+from click import Abort, progressbar
+
+from scout.adapter import MongoAdapter
+from scout.constants.panels import PRESELECTED_PANELAPP_PANEL_TYPE_SLUGS
+from scout.parse.panelapp import parse_panelapp_panel
+from scout.server.extensions import panelapp
+
+LOG = logging.getLogger(__name__)
+PANEL_NAME = "PANELAPP-GREEN"
+
+
+def load_panelapp_panel(
+    adapter: MongoAdapter,
+    panel_id: str = None,
+    institute: str = "cust000",
+    confidence: str = "green",
+):
+    """Load PanelApp panels into scout database."""
+
+    panel_ids = [panel_id]
+
+    if not panel_id:
+        LOG.info("Fetching all panel app panels")
+        panel_ids: List[str] = panelapp.get_panel_ids(signed_off=False)
+
+    ensembl_id_to_hgnc_id_map: Dict[str, int] = adapter.ensembl_to_hgnc_id_mapping()
+    hgnc_symbol_to_ensembl_id_map: Dict[int, str] = adapter.hgnc_symbol_ensembl_id_mapping()
+
+    for _ in panel_ids:
+        panel_info: dict = panelapp.get_panel(panel_id)
+        parsed_panel = parse_panelapp_panel(
+            panel_info=panel_info,
+            ensembl_id_to_hgnc_id_map=ensembl_id_to_hgnc_id_map,
+            hgnc_symbol_to_ensembl_id_map=hgnc_symbol_to_ensembl_id_map,
+            institute=institute,
+            confidence=confidence,
+        )
+
+        if len(parsed_panel["genes"]) == 0:
+            LOG.warning("Panel %s is missing genes. Skipping.", parsed_panel["display_name"])
+            continue
+
+        adapter.load_panel(parsed_panel=parsed_panel, replace=True)
+
+
+def get_panelapp_genes(
+    adapter: MongoAdapter, institute: str, panel_ids: List[str], types_filter: List[str]
+) -> Set[tuple]:
+    """Parse and collect genes from one or more panelApp panels."""
+
+    genes = set()
+    ensembl_id_to_hgnc_id_map: Dict[str, int] = adapter.ensembl_to_hgnc_id_mapping()
+    hgnc_symbol_to_ensembl_id_map: Dict[int, str] = adapter.hgnc_symbol_ensembl_id_mapping()
+
+    with progressbar(panel_ids, label="Parsing panels", length=len(panel_ids)) as panel_ids:
+        for panel_id in panel_ids:
+            panel_dict: dict = panelapp.get_panel(panel_id)
+            panel_type_slugs = [type["slug"] for type in panel_dict.get("types")]
+            # Parse panel only if it's of the expect type(s)
+            if not set(types_filter).intersection(panel_type_slugs):
+                continue
+
+            parsed_panel = parse_panelapp_panel(
+                panel_info=panel_dict,
+                ensembl_id_to_hgnc_id_map=ensembl_id_to_hgnc_id_map,
+                hgnc_symbol_to_ensembl_id_map=hgnc_symbol_to_ensembl_id_map,
+                institute=institute,
+                confidence="green",
+            )
+            genes.update(
+                {(gene["hgnc_id"], gene["hgnc_symbol"]) for gene in parsed_panel.get("genes")}
+            )
+
+    return genes
+
+
+def load_panelapp_green_panel(adapter: MongoAdapter, institute: str, force: bool, signed_off: bool):
+    """Load/Update the panel containing all Panelapp Green genes."""
+
+    def parse_types_filter(types_filter: str, available_types: List[str]) -> List[str]:
+        """Translate panel type input from users to panel type slugs."""
+        if not types_filter:
+            return PRESELECTED_PANELAPP_PANEL_TYPE_SLUGS
+        index_list = [int(typeint) - 1 for typeint in types_filter.replace(" ", "").split(",")]
+        return [available_types[i] for i in index_list]
+
+    # check and set panel version
+    old_panel = adapter.gene_panel(panel_id=PANEL_NAME)
+    green_panel = {
+        "panel_name": PANEL_NAME,
+        "display_name": "PanelApp Green Genes",
+        "institute": institute,
+        "version": float(math.floor(old_panel["version"]) + 1) if old_panel else 1.0,
+        "date": datetime.now(),
+    }
+
+    LOG.info("Fetching all PanelApp panels")
+
+    panel_ids = panelapp.get_panel_ids(signed_off=signed_off)
+    LOG.info(f"\n\nQuery returned {len(panel_ids)} panels\n")
+    LOG.info("Panels have the following associated types:")
+    available_types: List[str] = panelapp.get_panel_types()
+    for number, type in enumerate(available_types, 1):
+        LOG.info(f"{number}: {type}")
+    preselected_options_idx: List[str] = [
+        str(available_types.index(presel) + 1)
+        for presel in PRESELECTED_PANELAPP_PANEL_TYPE_SLUGS
+        if presel in available_types
+    ]
+    types_filter: str = input(
+        f"Please provide a comma-separated list of types you'd like to use to build your panel (leave blank to use the following types:{', '.join(preselected_options_idx)}):  "
+    )
+    types_filter: List[str] = parse_types_filter(
+        types_filter=types_filter, available_types=available_types
+    )
+    LOG.info(f"Collecting green genes from panels of type: {types_filter}")
+    green_panel["description"] = (
+        f"This panel contains green genes from {'signed off ' if signed_off else ''}panels of the following types: {', '.join(types_filter)}"
+    )
+    genes: Set[tuple] = get_panelapp_genes(
+        adapter=adapter, institute=institute, panel_ids=panel_ids, types_filter=types_filter
+    )
+    green_panel["genes"] = [{"hgnc_id": tup[0], "hgnc_symbol": tup[1]} for tup in genes]
+
+    # Do not update panel if new version contains less genes and force flag is False
+    if old_panel and len(old_panel.get("genes")) > len(green_panel["genes"]):
+        LOG.warning(
+            f"This new version of PANELAPP-GREEN contains less genes (n={len(green_panel['genes'])}) than the previous one (n={len(old_panel['genes'])})"
+        )
+        if force is False:
+            LOG.error("Aborting. Please use the force flag -f to update the panel anyway")
+            return
+    adapter.load_panel(parsed_panel=green_panel, replace=True)

scout/models/case/case_loading_models.py

@@ -557,10 +557,11 @@ class CaseLoader(BaseModel):
             images=custom_images.str_variants_images
         )
 
-        for key, images in custom_images.case_images.items():
-            custom_images.case_images[key] = set_custom_images(
-                images=custom_images.case_images[key]
-            )
+        if custom_images.case_images:
+            for key, images in custom_images.case_images.items():
+                custom_images.case_images[key] = set_custom_images(
+                    images=custom_images.case_images[key]
+                )
 
         return custom_images
 

scout/parse/panel.py

@@ -2,15 +2,9 @@
 
 import logging
 from datetime import datetime
-from typing import Dict, List, Optional
-
-from scout.constants import (
-    INCOMPLETE_PENETRANCE_MAP,
-    MODELS_MAP,
-    PANEL_GENE_INFO_MODELS,
-    PANEL_GENE_INFO_TRANSCRIPTS,
-    PANELAPP_CONFIDENCE_EXCLUDE,
-)
+from typing import List
+
+from scout.constants import PANEL_GENE_INFO_MODELS, PANEL_GENE_INFO_TRANSCRIPTS
 from scout.utils.date import get_date
 from scout.utils.handle import get_file_handle
 
@@ -266,114 +260,6 @@ def parse_gene_panel(
     return gene_panel
 
 
-def parse_panel_app_gene(
-    app_gene: dict,
-    ensembl_gene_hgnc_id_map: Dict[str, int],
-    hgnc_symbol_ensembl_gene_map: Dict[str, str],
-    confidence: str,
-) -> dict:
-    """Parse a panel app-formatted gene."""
-
-    gene_info = {}
-    confidence_level = app_gene["LevelOfConfidence"]
-    # Return empty gene if not confident gene
-    if confidence_level in PANELAPP_CONFIDENCE_EXCLUDE[confidence]:
-        return gene_info
-
-    hgnc_symbol = app_gene["GeneSymbol"]
-
-    ensembl_ids = app_gene["EnsembleGeneIds"]
-
-    if not ensembl_ids:  # This gene is probably tagged as ensembl_ids_known_missing on PanelApp
-        if hgnc_symbol in hgnc_symbol_ensembl_gene_map:
-            LOG.warning(
-                f"PanelApp gene {hgnc_symbol} does not contain Ensembl IDs. Using Ensembl IDs from internal gene collection instead."
-            )
-            ensembl_ids = [hgnc_symbol_ensembl_gene_map[hgnc_symbol]]
-        else:
-            LOG.warning(
-                f"PanelApp gene {hgnc_symbol} does not contain Ensembl IDs and gene symbol does not correspond to a gene in scout."
-            )
-
-    hgnc_ids = set(
-        ensembl_gene_hgnc_id_map.get(ensembl_id)
-        for ensembl_id in ensembl_ids
-        if ensembl_gene_hgnc_id_map.get(ensembl_id)
-    )
-    if not hgnc_ids:
-        LOG.warning("Gene %s does not exist in database. Skipping gene...", hgnc_symbol)
-        return gene_info
-
-    if len(hgnc_ids) > 1:
-        LOG.warning("Gene %s has unclear identifier. Choose random id", hgnc_symbol)
-
-    gene_info["hgnc_symbol"] = hgnc_symbol
-    for hgnc_id in hgnc_ids:
-        gene_info["hgnc_id"] = hgnc_id
-
-    gene_info["reduced_penetrance"] = INCOMPLETE_PENETRANCE_MAP.get(app_gene["Penetrance"])
-
-    inheritance_models = []
-    for model in MODELS_MAP.get(app_gene["ModeOfInheritance"], []):
-        inheritance_models.append(model)
-
-    gene_info["inheritance_models"] = inheritance_models
-
-    return gene_info
-
-
-def parse_panel_app_panel(
-    panel_info: dict,
-    ensembl_gene_hgnc_id_map: Dict[str, int],
-    hgnc_symbol_ensembl_gene_map: Dict[str, str],
-    institute: Optional[str] = "cust000",
-    panel_type: Optional[str] = "clinical",
-    confidence: Optional[str] = "green",
-) -> dict:
-    """Parse a PanelApp panel
-
-    Args:
-        panel_info(dict)
-        hgnc_map(dict): Map from symbol to hgnc ids
-        institute(str)
-        panel_type(str)
-        confidence(str): enum green|amber|red
-
-    Returns:
-        gene_panel(dict)
-    """
-    date_format = "%Y-%m-%dT%H:%M:%S.%f"
-
-    gene_panel = {}
-    gene_panel["version"] = float(panel_info["version"])
-    gene_panel["date"] = get_date(panel_info["Created"][:-1], date_format=date_format)
-    gene_panel["display_name"] = " - ".join(
-        [panel_info["SpecificDiseaseName"], f"[{confidence.upper()}]"]
-    )
-    gene_panel["institute"] = institute
-    gene_panel["panel_type"] = panel_type
-
-    LOG.info("Parsing panel %s", gene_panel["display_name"])
-
-    gene_panel["genes"] = []
-
-    nr_excluded = 0
-    nr_genes = 0
-    for nr_genes, gene in enumerate(panel_info["Genes"], 1):
-        gene_info = parse_panel_app_gene(
-            gene, ensembl_gene_hgnc_id_map, hgnc_symbol_ensembl_gene_map, confidence
-        )
-        if not gene_info:
-            nr_excluded += 1
-            continue
-        gene_panel["genes"].append(gene_info)
-
-    LOG.info("Number of genes in panel %s", nr_genes)
-    LOG.info("Number of genes exluded due to confidence threshold: %s", nr_excluded)
-
-    return gene_panel
-
-
 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

scout/parse/panelapp.py

@@ -0,0 +1,112 @@
+"""Code to parse panel information"""
+
+import logging
+from typing import Dict, List, Optional
+
+from scout.constants import INCOMPLETE_PENETRANCE_MAP, MODELS_MAP, PANELAPP_CONFIDENCE_EXCLUDE
+from scout.utils.date import get_date
+
+LOG = logging.getLogger(__name__)
+
+
+def parse_panel_app_gene(
+    panelapp_gene: dict,
+    ensembl_gene_hgnc_id_map: Dict[str, int],
+    hgnc_symbol_ensembl_gene_map: Dict[str, str],
+    confidence: str,
+) -> dict:
+    """Parse a panel app-formatted gene."""
+    gene_info = {}
+    confidence_level = panelapp_gene["confidence_level"]
+    # Return empty gene if not confident gene
+    if confidence_level in PANELAPP_CONFIDENCE_EXCLUDE[confidence]:
+        return gene_info
+
+    hgnc_symbol = panelapp_gene["gene_data"]["gene_symbol"]
+    ensembl_ids = [
+        version["ensembl_id"]
+        for genome in panelapp_gene["gene_data"]["ensembl_genes"].values()
+        for version in genome.values()
+    ]
+
+    if not ensembl_ids:  # This gene is probably tagged as ensembl_ids_known_missing on PanelApp
+        if hgnc_symbol in hgnc_symbol_ensembl_gene_map:
+            LOG.warning(
+                f"PanelApp gene {hgnc_symbol} does not contain Ensembl IDs. Using Ensembl IDs from internal gene collection instead."
+            )
+            ensembl_ids = [hgnc_symbol_ensembl_gene_map[hgnc_symbol]]
+        else:
+            LOG.warning(
+                f"PanelApp gene {hgnc_symbol} does not contain Ensembl IDs and gene symbol does not correspond to a gene in scout."
+            )
+
+    hgnc_ids = set(
+        ensembl_gene_hgnc_id_map.get(ensembl_id)
+        for ensembl_id in ensembl_ids
+        if ensembl_gene_hgnc_id_map.get(ensembl_id)
+    )
+    if not hgnc_ids:
+        LOG.warning("Gene %s does not exist in database. Skipping gene...", hgnc_symbol)
+        return gene_info
+
+    if len(hgnc_ids) > 1:
+        LOG.warning("Gene %s has unclear identifier. Choose random id", hgnc_symbol)
+
+    gene_info["hgnc_symbol"] = hgnc_symbol
+    for hgnc_id in hgnc_ids:
+        gene_info["hgnc_id"] = hgnc_id
+
+    gene_info["reduced_penetrance"] = INCOMPLETE_PENETRANCE_MAP.get(panelapp_gene["penetrance"])
+
+    inheritance_models = []
+    for model in MODELS_MAP.get(panelapp_gene["mode_of_inheritance"], []):
+        inheritance_models.append(model)
+
+    gene_info["inheritance_models"] = inheritance_models
+
+    return gene_info
+
+
+def parse_panelapp_panel(
+    panel_info: dict,
+    ensembl_id_to_hgnc_id_map: Dict[str, int],
+    hgnc_symbol_to_ensembl_id_map: Dict[str, str],
+    institute: Optional[str] = "cust000",
+    confidence: Optional[str] = "green",
+) -> dict:
+    """Parse a PanelApp panel"""
+
+    date_format = "%Y-%m-%dT%H:%M:%S.%f"
+
+    gene_panel = {}
+    panel_id = str(panel_info["id"])
+    if confidence != "green":
+        gene_panel["panel_id"] = "_".join([panel_id, confidence])
+    else:  # This way the old green panels will be overwritten, instead of creating 2 sets of green panels, old and new
+        gene_panel["panel_id"] = panel_id
+
+    gene_panel["version"] = float(panel_info["version"])
+    gene_panel["date"] = get_date(panel_info["version_created"][:-1], date_format=date_format)
+    gene_panel["display_name"] = " - ".join([panel_info["name"], f"[{confidence.upper()}]"])
+    gene_panel["institute"] = institute
+    gene_panel["panel_type"] = ("clinical",)
+
+    LOG.info("Parsing panel %s", gene_panel["display_name"])
+
+    gene_panel["genes"] = []
+
+    nr_excluded = 0
+    nr_genes = 0
+    for nr_genes, gene in enumerate(panel_info["genes"], 1):
+        gene_info = parse_panel_app_gene(
+            gene, ensembl_id_to_hgnc_id_map, hgnc_symbol_to_ensembl_id_map, confidence
+        )
+        if not gene_info:
+            nr_excluded += 1
+            continue
+        gene_panel["genes"].append(gene_info)
+
+    LOG.info("Number of genes in panel %s", nr_genes)
+    LOG.info("Number of genes excluded due to confidence threshold: %s", nr_excluded)
+
+    return gene_panel

scout/parse/variant/clnsig.py

@@ -1,9 +1,14 @@
 import logging
+from typing import Dict, List, Optional, Union
+
+import cyvcf2
 
 LOG = logging.getLogger(__name__)
 
 
-def parse_clnsig(variant, transcripts=None):
+def parse_clnsig(
+    variant: cyvcf2.Variant, transcripts: Optional[dict] = None
+) -> List[Dict[str, Union[str, int]]]:
     """Get the clnsig information
 
     The clinvar format has changed several times and this function will try to parse all of them.
@@ -15,12 +20,7 @@ def parse_clnsig(variant, transcripts=None):
     sometimes with CLNVID.
     This function parses also Clinvar annotations performed by VEP (CSQ field, parsed transcripts required)
 
-    Args:
-        variant(cyvcf2.Variant)
-        transcripts(iterable(dict))
-
-    Returns:
-        clnsig_accsessions(list(dict)): A list with clnsig accessions
+    Returns a list with clnsig accessions
     """
     transcripts = transcripts or []
     acc = variant.INFO.get("CLNACC", variant.INFO.get("CLNVID", ""))
@@ -87,33 +87,42 @@ def parse_clnsig(variant, transcripts=None):
     return clnsig_accessions
 
 
-def is_pathogenic(variant):
+def is_pathogenic(variant: cyvcf2.Variant):
     """Check if a variant has the clinical significance to be loaded
 
     We want to load all variants that are in any of the predefined categories regardless of rank
     scores etc.
 
-    Args:
-        variant(cyvcf2.Variant)
+    To avoid parsing much, we first quickly check if we have a string match to substrings in
+    all relevant categories, that are somewhat rare in the CSQ strings in general. If not,
+    we check more carefully.
+
+    We include the old style numerical categories as well for backwards compatibility.
 
     Returns:
         bool: If variant should be loaded based on clinvar or not
     """
 
-    load_categories = {
-        "pathogenic",
-        "likely_pathogenic",
-        "conflicting_interpretations_of_pathogenicity",
-        "conflicting_interpretations",
-    }
+    quick_load_categories = {"pathogenic", "conflicting_"}
 
     # check if VEP-annotated field contains clinvar pathogenicity info
     vep_info = variant.INFO.get("CSQ")
     if vep_info:
-        for category in load_categories:
+        for category in quick_load_categories:
             if category in vep_info.lower():
                 return True
 
+    load_categories: set = {
+        "pathogenic",
+        "likely_pathogenic",
+        "conflicting_classifications_of_pathogenicity",
+        "conflicting_interpretations_of_pathogenicity",
+        "conflicting_interpretations",
+        4,
+        5,
+        8,
+    }
+
     # Otherwise check if clinvar pathogenicity status is in INFO field
     clnsig_accessions = parse_clnsig(variant)
 
@@ -121,8 +130,4 @@ def is_pathogenic(variant):
         clnsig = annotation["value"]
         if clnsig in load_categories:
             return True
-        if isinstance(clnsig, int):
-            if clnsig == 4 or clnsig == 5:
-                return True
-
     return False

scout/parse/variant/genotype.py

@@ -291,11 +291,12 @@ def get_split_reads(variant, pos):
 
 
 def get_alt_frequency(variant, pos):
-    """ """
-    alt_frequency = float(variant.gt_alt_freqs[pos])
-    if alt_frequency == -1:
-        if "AF" in variant.FORMAT:
-            alt_frequency = float(variant.format("AF")[pos][0])
+    """AF - prioritise caller AF if set in FORMAT (e.g. DeepVariant does an INFO field)"""
+    if "AF" in variant.FORMAT:
+        alt_frequency = float(variant.format("AF")[pos][0])
+    else:
+        alt_frequency = float(variant.gt_alt_freqs[pos])
+
     return alt_frequency
 
 

scout/server/blueprints/alignviewers/controllers.py

@@ -297,13 +297,13 @@ def set_common_tracks(display_obj, build):
             display_obj["custom_tracks"].append(track)
 
 
-def set_sample_tracks(display_obj, case_groups, chromosome):
+def set_sample_tracks(display_obj: dict, case_groups: list, chromosome: str):
     """Set up individual-specific alignment tracks (bam/cram files)
 
-    Args:
-        display_obj(dict): dictionary containing all tracks info
-        case_groups(list): a list of case dictionaries
-        chromosome(str) [1-22],X,Y,M or "All"
+    Given a dictionary containing all tracks info (display_obj), a list of case group dictionaries
+    A chromosome string argument is used to check if we should look at mt alignment files for MT.
+
+    A missing file is indicated with the string "missing", and no track is made for such entries.
     """
     sample_tracks = []
 
@@ -321,6 +321,8 @@ def set_sample_tracks(display_obj, case_groups, chromosome):
             return
 
         for count, sample in enumerate(case.get("sample_names")):
+            if case[track_items][count] == "missing" or case[track_index_items][count] == "missing":
+                continue
             sample_tracks.append(
                 {
                     "name": sample,

scout/server/blueprints/alignviewers/templates/alignviewers/utils.html

@@ -1,5 +1,5 @@
 {% macro igv_script() %}
   <link rel="shortcut icon" href="//igv.org/web/img/favicon.ico">
   <!-- IGV JS-->
-  <script src="https://cdn.jsdelivr.net/npm/igv@3.0.5/dist/igv.min.js" integrity="sha512-v/9h2zZ8sRzSmIkMWHq/9Zbs54d2P/wd15/r0peNTqZn7uD/VfrwmeyT4pfBe94nbF9mQhbU5FI+zIXqqnPRpw==" crossorigin="anonymous"></script>
+  <script src="https://cdn.jsdelivr.net/npm/igv@3.0.9/dist/igv.min.js" integrity="sha512-vcMdgqBb5jsj6fAIlBMkDe3riA5meRJARkXtDFAl+5/jm5TxL6agAFq8Ek8LzrHtLncs40Qa8s98awdkINjy+Q==" crossorigin="anonymous"></script>
 {% endmacro %}

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

@@ -30,61 +30,68 @@
   <div class="card col-md-12">
     <h4 class="mt-3">Case: {{case.display_name}}</h4>
     <div class="card-body">
-
       <div class="row">
-            <div class="col-xs-12 col-md-12">{{ smn_individuals_table(case, institute, tissue_types) }}</div>
-        </div> <!-- end of div class row -->
-        <div class="row">
-          <div class="col-md-4">
-            {% if case.madeline_info and case.individuals|length > 1 %}
-              {{ pedigree_panel() }}
-            {% else %}
-              <p>No pedigree picture available.</p>
-            {% endif %}
-          </div>
-          <div class="col-md-8">
-            {{ synopsis_panel() }}
-            <div class="panel-default">
-            {{ comments_panel(institute, case, current_user, comments) }}
-            </div>
+        <div class="col-xs-12 col-md-12">{{ smn_individuals_table(case, institute, tissue_types) }}</div>
+      </div> <!-- end of div class row -->
+      <div class="row">
+        <div class="col-md-4">
+          {% if case.madeline_info and case.individuals|length > 1 %}
+            {{ pedigree_panel() }}
+          {% else %}
+            <p>No pedigree picture available.</p>
+          {% endif %}
+        </div>
+        <div class="col-md-8">
+          {{ synopsis_panel() }}
+          <div class="panel-default">
+          {{ comments_panel(institute, case, current_user, comments) }}
           </div>
-        </div> <!-- end of div class row -->
+        </div>
+      </div> <!-- end of div class row -->
 
-        <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) }}">
-              <input type="hidden" id="hgnc_symbols" name="hgnc_symbols" value="SMN1, SMN2"></input>
-              <input type="hidden" id="gene_panels" name="gene_panels" value="['']"></input>
-              <span><button type="submit" class="btn btn-secondary btn-sm" target="_blank" rel="noopener" data-bs-toggle="tooltip" title="SNV and INDEL variants view filtered for the genes SMN1 and SMN2">SNVs</button></span>
-            </form>
-          </span>
-          {% endif %}
-          {% if case.vcf_files.vcf_sv %}
+      <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) }}">
+            <input type="hidden" id="hgnc_symbols" name="hgnc_symbols" value="SMN1, SMN2"></input>
+            <input type="hidden" id="gene_panels" name="gene_panels" value="['']"></input>
+            <span><button type="submit" class="btn btn-secondary btn-sm" target="_blank" rel="noopener" data-bs-toggle="tooltip" title="SNV and INDEL variants view filtered for the genes SMN1 and SMN2">SNVs</button></span>
+          </form>
+        </span>
+        {% endif %}
+        {% if case.vcf_files.vcf_sv %}
           <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>
+              <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>
             </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>
+        {% endif %}
 
-        <div class="row">
-          <div class="col-sm-12">{{activity_panel(events)}}</div>
-        </div>
+        <span class="me-3"
+          {% if not case.bam_files %}title="Alignment file(s) missing" data-bs-toggle="tooltip"{% endif %}>
+          <a 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"
+            class="btn btn-secondary btn-sm text-white{% if not case.bam_files %} disabled{% endif %}">
+            IGV DNA SMN1
+          </a>
+        </span>
+        <span class="me-3"
+          {% if not case.bam_files %}title="Alignment file(s) missing" data-bs-toggle="tooltip"{% endif %}>
+          <a 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"
+            class="btn btn-secondary btn-sm text-white{% if not case.bam_files %} disabled{% endif %}">
+            IGV DNA SMN2
+          </a>
+        </span>
+      </span>
 
-        {{ modal_synopsis() }}
+      <div class="row">
+        <div class="col-sm-12">{{activity_panel(events)}}</div>
+      </div>
+
+      {{ modal_synopsis() }}
     </div> <!-- end of card body -->
   </div> <!-- end of card div-->
-</div>
 </div> <!-- end of div class col -->
 {% endmacro %}