Merge pull request #1636 from nuno-agostinho/fix/svtype

Fix SVTYPE when using IUPAC nucleotide codes
Ensembl · Apr 8, 2024 · 5dafe4b · 5dafe4b
2 parents b06c889 + 1ec63c4
commit 5dafe4b
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Showing 3 changed files with 11 additions and 5 deletions.
diff --git a/modules/Bio/EnsEMBL/VEP/Parser.pm b/modules/Bio/EnsEMBL/VEP/Parser.pm
@@ -723,7 +723,7 @@ sub get_SO_term {
   my $res = $terms{$abbrev};
   ## unsupported SV types
   if ($self->isa('Bio::EnsEMBL::VEP::Parser')) {
-    $self->skipped_variant_msg("$abbrev type is not supported") unless $res;
+    $self->skipped_variant_msg("$abbrev is not a supported structural variant type") unless $res;
   }
   return $res;
 }

diff --git a/modules/Bio/EnsEMBL/VEP/Parser/VCF.pm b/modules/Bio/EnsEMBL/VEP/Parser/VCF.pm
@@ -460,9 +460,15 @@ sub create_StructuralVariationFeatures {
     $parser->get_IDs,
   );
 
-  ## get structural variant type from SVTYPE tag (deprecated in VCF 4.4) or ALT
+  ## get structural variant type from ALT or (deprecated) SVTYPE tag
   my $alt = join("/", @$alts);
-  my $type = $alt ne '.' ? $alt : $info->{SVTYPE};
+  my $type = $alt;
+
+  # replace with SVTYPE tag if ALT does not follow VCF 4.4 specs
+  if ($info->{SVTYPE} && $alt !~ /^<?(DEL|INS|DUP|INV|CNV|CN=?[0-9]+)/) {
+    $type = $info->{SVTYPE};
+  }
+
   my $so_term = $self->get_SO_term($type);
   unless ($so_term) {
     $skip_line = 1;

diff --git a/t/Parser_VCF.t b/t/Parser_VCF.t
@@ -621,14 +621,14 @@ is_deeply($cvf, bless( {
                  'inner_start' => '774570',
                  'strand' => 1,
                  'seq_region_end' => 828435,
-                 'class_SO_term' => '<CPX>',
+                 'class_SO_term' => 'CPX',
                  'variation_name' => 'gnomAD_v2_CPX_1_1',
                  'start' => 774570
                },
                 'Bio::EnsEMBL::Variation::StructuralVariationFeature' ) , 'StructuralVariationFeature - CPX skipped');
 
 
-like($tmp, qr/CPX type is not supported/, 'StructuralVariationFeature - skip CPX warning');
+like($tmp, qr/CPX is not a supported structural variant type/, 'StructuralVariationFeature - skip CPX warning');
 
 open(STDERR, ">&SAVE") or die "Can't restore STDERR\n";