From 5d0aa0b7f164c18fc86548947e4ff3c16a45ac49 Mon Sep 17 00:00:00 2001
From: Nuno Agostinho <nuno@ebi.ac.uk>
Date: Wed, 12 Jun 2024 09:26:29 +0100
Subject: [PATCH] Fix warning when using SV in VCF format with 5 fields

---
 modules/Bio/EnsEMBL/VEP/Parser/VCF.pm | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/modules/Bio/EnsEMBL/VEP/Parser/VCF.pm b/modules/Bio/EnsEMBL/VEP/Parser/VCF.pm
index bb5972e12..1c2e061a9 100644
--- 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);