Merge pull request Ensembl#1712 from nakib103/update_gnomad

Add gnomAD v4.1 populations
likhitha-surapaneni · Jul 16, 2024 · 17471a7 · 17471a7
2 parents b2b4ce1 + 211f319
commit 17471a7
Showing 1 changed file with 19 additions and 9 deletions.
diff --git a/modules/Bio/EnsEMBL/VEP/Pipeline/DumpVEP/DumpVEP_conf.pm b/modules/Bio/EnsEMBL/VEP/Pipeline/DumpVEP/DumpVEP_conf.pm
@@ -123,12 +123,22 @@ sub default_options {
                 version => 'phase3'
               },
               {
-                file => $self->o('data_dir').'/gnomAD/v2.1/grch37/exomes/gnomad.exomes.r2.1.sites.chr+++CHR+++_noVEP.vcf.gz',
-                pops => ['', qw(afr amr asj eas fin nfe oth sas)],
+                file => $self->o('data_dir').'/gnomAD/v4.1/grch37/exomes/gnomad.exomes.v4.1.sites.grch37.chr+++CHR+++_trimmed_liftover.vcf.gz',
+                pops => ['', qw(afr amr asj eas fin nfe remaining sas mid)],
                 chroms => [qw(1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y)],
                 name => 'gnomADe',
                 prefix => 'gnomADe',
-                version => 'r2.1',
+                version => 'v4.1',
+                use_chr_prefix => 1,
+              },
+              {
+                file => $self->o('data_dir').'/gnomAD/v4.1/grch37/genomes/gnomad.genomes.v4.1.sites.grch37.chr+++CHR+++_trimmed_liftover.vcf.gz',
+                pops => ['', qw(afr amr asj eas fin nfe remaining sas mid ami)],
+                chroms => [qw(1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y)],
+                name => 'gnomADg',
+                prefix => 'gnomADg',
+                version => 'v4.1',
+                use_chr_prefix => 1,
               },
             ],
           },
@@ -143,21 +153,21 @@ sub default_options {
                 version => 'phase3'
               },
               {
-                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)],
+                file => $self->o('data_dir').'/gnomAD/v4.1/grch38/exomes/gnomad.exomes.v4.1.sites.chr+++CHR+++_trimmed.vcf.bgz',
+                pops => ['', qw(afr amr asj eas fin nfe remaining sas mid)],
                 chroms => [qw(1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y)],
                 name => 'gnomADe',
                 prefix => 'gnomADe',
-                version => 'r2.1.1',
+                version => 'v4.1',
                 use_chr_prefix => 1,
               },
               {
-                file => $self->o('data_dir').'/gnomAD/v3.1.2/grch38/genomes/gnomad.genomes.v3.1.2.sites.chr+++CHR+++_trimmed_info.vcf.bgz',
-                pops => ['', qw(afr ami amr asj eas fin mid nfe oth sas)],
+                file => $self->o('data_dir').'/gnomAD/v4.1/grch38/genomes/gnomad.genomes.v4.1.sites.chr+++CHR+++_trimmed.vcf.bgz',
+                pops => ['', qw(afr ami amr asj eas fin mid nfe remaining sas)],
                 chroms => [qw(1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y)],
                 name => 'gnomADg',
                 prefix => 'gnomADg',
-                version => 'v3.1.2',
+                version => 'v4.1',
                 use_chr_prefix => 1,
               },
             ],