From 211f319603c554700524a9c8c0c06c20c036000f Mon Sep 17 00:00:00 2001 From: Syed Nakib Hossain Date: Mon, 1 Jul 2024 10:55:27 +0100 Subject: [PATCH] Add gnomAD v4.1 populations --- .../VEP/Pipeline/DumpVEP/DumpVEP_conf.pm | 28 +++++++++++++------ 1 file changed, 19 insertions(+), 9 deletions(-) diff --git a/modules/Bio/EnsEMBL/VEP/Pipeline/DumpVEP/DumpVEP_conf.pm b/modules/Bio/EnsEMBL/VEP/Pipeline/DumpVEP/DumpVEP_conf.pm index 6576dd29d..4ff9857de 100644 --- 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, }, ],