Merge branch 'postreleasefix/104' into release/104

Ensembl · Apr 1, 2021 · 2b97315 · 2b97315
2 parents 26ec44e + 5a06f79
commit 2b97315
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Showing 2 changed files with 5 additions and 1 deletion.
diff --git a/modules/Bio/EnsEMBL/VEP/Pipeline/DumpVEP/DumpVEP_conf.pm b/modules/Bio/EnsEMBL/VEP/Pipeline/DumpVEP/DumpVEP_conf.pm
@@ -158,11 +158,11 @@ sub default_options {
               # },
               {
                 file => $self->o('data_dir').'/gnomAD/v2.1.1/grch38/exomes/gnomad.exomes.r2.1.1.sites.+++CHR+++.liftover_grch38_no_VEP.vcf.gz',
-
                 pops => ['', qw(afr amr asj eas fin nfe oth sas)],
                 name => 'gnomAD',
                 prefix => 'gnomAD',
                 version => 'r2.1.1',
+                use_chr_prefix => 1,
               },
             ],
           },

diff --git a/modules/Bio/EnsEMBL/VEP/Pipeline/DumpVEP/Dumper/Variation.pm b/modules/Bio/EnsEMBL/VEP/Pipeline/DumpVEP/Dumper/Variation.pm
@@ -291,6 +291,10 @@ sub freqs_from_vcf {
     my $parser = $self->{_vcf_parsers}->{$file} ||= Bio::EnsEMBL::IO::Parser::VCF4Tabix->open($file);
     next unless $parser;
 
+    if (defined $vcf_conf->{use_chr_prefix} && $vcf_conf->{use_chr_prefix}) {
+      $chr = "chr$chr";
+    }
+
     $parser->seek($chr, $list[0]->{start} - 1, $list[-1]->{end} + 1);
 
     while($parser->next) {