Merge pull request Ensembl#1700 from nuno-agostinho/fix/SV-VCF-5fields

Fix warning when using SV in VCF format with 5 fields
likhitha-surapaneni · Jun 24, 2024 · 52e0065 · 52e0065
2 parents 627d964 + 5d0aa0b
commit 52e0065
Showing 1 changed file with 4 additions and 0 deletions.
diff --git a/modules/Bio/EnsEMBL/VEP/Parser/VCF.pm b/modules/Bio/EnsEMBL/VEP/Parser/VCF.pm
@@ -459,6 +459,10 @@ sub create_StructuralVariationFeatures {
     $parser->get_info,
     $parser->get_IDs,
   );
+  # VEP accepts VCF input with the first 5 fields: fill the remaining mandatory fields to avoid warnings
+  $record->[5] ||= '.';
+  $record->[6] ||= '.';
+  $record->[7] ||= '.';
 
   ## get structural variant type from ALT or (deprecated) SVTYPE tag
   my $alt = join("/", @$alts);