added gnomad popmax AC

GC-HBOC · Nov 8, 2023 · a2c47de · a2c47de
1 parent b49231b
commit a2c47de
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Showing 3 changed files with 5 additions and 7 deletions.
diff --git a/src/annotation_service/annotation_jobs/annotate_from_vcf_job.py b/src/annotation_service/annotation_jobs/annotate_from_vcf_job.py
@@ -60,6 +60,7 @@ def save_to_db(self, info, variant_id, conn):
         self.insert_annotation(variant_id, info, "GnomAD_popmax=", recent_annotation_ids['gnomad_popmax'], conn, value_modifier_function = lambda value : value.upper())
         self.insert_annotation(variant_id, info, "GnomAD_AF_popmax=", recent_annotation_ids['gnomad_popmax_AF'], conn)
         self.insert_annotation(variant_id, info, "GnomADm_AC_hom=", recent_annotation_ids['gnomadm_ac_hom'], conn)
+        self.insert_annotation(variant_id, info, "GnomAD_AC_popmax=", recent_annotation_ids['gnomad_popmax_AC'], conn)
 
         self.insert_annotation(variant_id, info, "BRCA_exchange_clin_sig_short=", recent_annotation_ids['brca_exchange_clinical_significance'], conn, value_modifier_function = lambda value : value.replace('_', ' ').replace(',', ';'))
 
@@ -164,7 +165,7 @@ def write_vcf_annoate_config(self, one_variant):
 
         ## add gnomAD annotation
         if self.job_config['do_gnomad']:
-            config_file.write(paths.gnomad_path + "\tGnomAD\tAF,AC,hom,hemi,het,popmax,AF_popmax\t\n")
+            config_file.write(paths.gnomad_path + "\tGnomAD\tAF,AC,hom,hemi,het,popmax,AF_popmax,AC_popmax\t\n")
             config_file.write(paths.gnomad_m_path + "\tGnomADm\tAC_hom\t\n")
 
         ## add BRCA_exchange clinical significance

diff --git a/src/common/models.py b/src/common/models.py
@@ -109,6 +109,7 @@ class AllAnnotations:
     gnomad_popmax: Annotation = None
     gnomadm_ac_hom: Annotation = None
     gnomad_popmax_AF: Annotation = None
+    gnomad_popmax_AC: Annotation = None
 
     brca_exchange_clinical_significance: Annotation = None
     arup_classification: Annotation = None
@@ -881,13 +882,7 @@ def get_preferred_transcripts(self):
         if len(sortable_dict) == 0:
             return None
 
-        #print("sortable dict:")
-        #print(sortable_dict)
         transcripts_sorted, consequences_sorted = functions.sort_transcript_dict(sortable_dict)
-        #print("transcripts_sorted:")
-        #print(transcripts_sorted)
-        #print("consequences_sorted:")
-        #print(consequences_sorted)
         result.append(consequences_sorted.pop(0)) # always append the first one
         for consequence in consequences_sorted: # scan for all mane select transcripts
             if consequence.transcript.is_mane_select:

diff --git a/src/frontend_celery/webapp/templates/index.html b/src/frontend_celery/webapp/templates/index.html
@@ -104,13 +104,15 @@ <h4>Changelog</h4>
             <li>Added cDNA search</li>
             <li>Update search help</li>
             <li>Added COSMIC COSV ids & moved COSMIC links from consequence table to the variant banner.</li>
+            <li>Added GnomAD popmax allele count (AC) annotation</li>
         </ul>
         Bugfixes:
         <ul>
             <li>Fixed a bug where the "gene", "your classification" and "consensus classification" columns were not clickable</li>
             <li>Fixed a bug where in some cases some ClinVar submissions were not annotated</li>
             <li>Fixed a bug which caused some annotations to be erroneous, when importing variants from HerediCare</li>
             <li>Fixed status of deleted VIDs upon variant import</li>
+            <li>In some cases the consequence was duplicated in the variant banner.</li>
         </ul>
         Known issues:
         <ul>