diff --git a/lib/EnsEMBL/REST/Controller/VEP.pm b/lib/EnsEMBL/REST/Controller/VEP.pm
index 58e8e39a..69b429a8 100644
--- a/lib/EnsEMBL/REST/Controller/VEP.pm
+++ b/lib/EnsEMBL/REST/Controller/VEP.pm
@@ -455,6 +455,7 @@ sub _configure_plugins {
push @params, $param;
}
+ # CADD - check if species is chicken and provide appropriate file based on that
elsif(lc $module eq 'cadd' && $c->stash->{species} eq "gallus_gallus_gca000002315v5"){
next unless $param =~ /^snv_chicken_rjf=/;
@@ -464,6 +465,16 @@ sub _configure_plugins {
push @params, $param;
}
+ # CADD - check if species is turkey and provide appropriate file based on that
+ elsif(lc $module eq 'cadd' && $c->stash->{species} eq "meleagris_gallopavo"){
+ next unless $param =~ /^snv_turkey=/;
+
+ my $param_aux = $param;
+ $param_aux =~ s/snv_turkey=//;
+ $param = 'snv=' . $param_aux;
+
+ push @params, $param;
+ }
elsif(lc $module eq 'cadd' && ($user_config->{$module} eq "snv_indels" || $user_config->{$module} eq "1")){
next unless ($param =~ /^snv=/ || $param =~ /^indels=/);
push @params, $param;
diff --git a/root/documentation/vep.conf b/root/documentation/vep.conf
index fbe0023f..d6eb669f 100644
--- a/root/documentation/vep.conf
+++ b/root/documentation/vep.conf
@@ -312,7 +312,7 @@
type=Boolean
- description=Include CADD (Combined Annotation Dependent Depletion) deleteriousness scores for single nucleotide variants (also supports sus_scrofa and chicken (red jungle fowl)), indels and structural variants (only supported in GRCh38). Following options can be given: snv, indels, snv_indels, and sv. Providing 1 is also supported which is same as providing snv_indels. Caution to be taken while using snv, indels or snv_indels options with structural variants as input. It can match unnecessary huge amount of lines in annotation file and in such cases no CADD annotation will be made. See license. (plugin details)
+ description=Include CADD (Combined Annotation Dependent Depletion) deleteriousness scores for single nucleotide variants (also supports sus_scrofa, chicken (red jungle fowl) and turkey), indels and structural variants (only supported in GRCh38). Following options can be given: snv, indels, snv_indels, and sv. Providing 1 is also supported which is same as providing snv_indels. Caution to be taken while using snv, indels or snv_indels options with structural variants as input. It can match unnecessary huge amount of lines in annotation file and in such cases no CADD annotation will be made. See license. (plugin details)
default=0
example=snv_indels,1
@@ -682,7 +682,7 @@
type=Boolean
- description=Include CADD (Combined Annotation Dependent Depletion) deleteriousness scores for single nucleotide variants (also supports sus_scrofa and chicken (red jungle fowl)), indels and structural variants (only supported in GRCh38). Following options can be given: snv, indels, snv_indels, and sv. Providing 1 is also supported which is same as providing snv_indels. Caution to be taken while using snv, indels or snv_indels options with structural variants as input. It can match unnecessary huge amount of lines in annotation file and in such cases no CADD annotation will be made. See license. (plugin details)
+ description=Include CADD (Combined Annotation Dependent Depletion) deleteriousness scores for single nucleotide variants (also supports sus_scrofa, chicken (red jungle fowl) and turkey), indels and structural variants (only supported in GRCh38). Following options can be given: snv, indels, snv_indels, and sv. Providing 1 is also supported which is same as providing snv_indels. Caution to be taken while using snv, indels or snv_indels options with structural variants as input. It can match unnecessary huge amount of lines in annotation file and in such cases no CADD annotation will be made. See license. (plugin details)
default=0
example=snv_indels,1
@@ -1040,7 +1040,7 @@
type=Boolean
- description=Include CADD (Combined Annotation Dependent Depletion) deleteriousness scores for single nucleotide variants (also supports sus_scrofa and chicken (red jungle fowl)), indels and structural variants (only supported in GRCh38). Following options can be given: snv, indels, snv_indels, and sv. Providing 1 is also supported which is same as providing snv_indels. Caution to be taken while using snv, indels or snv_indels options with structural variants as input. It can match unnecessary huge amount of lines in annotation file and in such cases no CADD annotation will be made. See license. (plugin details)
+ description=Include CADD (Combined Annotation Dependent Depletion) deleteriousness scores for single nucleotide variants (also supports sus_scrofa, chicken (red jungle fowl) and turkey), indels and structural variants (only supported in GRCh38). Following options can be given: snv, indels, snv_indels, and sv. Providing 1 is also supported which is same as providing snv_indels. Caution to be taken while using snv, indels or snv_indels options with structural variants as input. It can match unnecessary huge amount of lines in annotation file and in such cases no CADD annotation will be made. See license. (plugin details)
default=0
example=snv_indels,1
@@ -1392,7 +1392,7 @@
type=Boolean
- description=Include CADD (Combined Annotation Dependent Depletion) deleteriousness scores for single nucleotide variants (also supports sus_scrofa and chicken (red jungle fowl)), indels and structural variants (only supported in GRCh38). Following options can be given: snv, indels, snv_indels, and sv. Providing 1 is also supported which is same as providing snv_indels. Caution to be taken while using snv, indels or snv_indels options with structural variants as input. It can match unnecessary huge amount of lines in annotation file and in such cases no CADD annotation will be made. See license. (plugin details)
+ description=Include CADD (Combined Annotation Dependent Depletion) deleteriousness scores for single nucleotide variants (also supports sus_scrofa, chicken (red jungle fowl) and turkey), indels and structural variants (only supported in GRCh38). Following options can be given: snv, indels, snv_indels, and sv. Providing 1 is also supported which is same as providing snv_indels. Caution to be taken while using snv, indels or snv_indels options with structural variants as input. It can match unnecessary huge amount of lines in annotation file and in such cases no CADD annotation will be made. See license. (plugin details)
default=0
example=snv_indels,1
@@ -1755,7 +1755,7 @@
type=Boolean
- description=Include CADD (Combined Annotation Dependent Depletion) deleteriousness scores for single nucleotide variants (also supports sus_scrofa and chicken (red jungle fowl)), indels and structural variants (only supported in GRCh38). Following options can be given: snv, indels, snv_indels, and sv. Providing 1 is also supported which is same as providing snv_indels. Caution to be taken while using snv, indels or snv_indels options with structural variants as input. It can match unnecessary huge amount of lines in annotation file and in such cases no CADD annotation will be made. See license. (plugin details)
+ description=Include CADD (Combined Annotation Dependent Depletion) deleteriousness scores for single nucleotide variants (also supports sus_scrofa, chicken (red jungle fowl) and turkey), indels and structural variants (only supported in GRCh38). Following options can be given: snv, indels, snv_indels, and sv. Providing 1 is also supported which is same as providing snv_indels. Caution to be taken while using snv, indels or snv_indels options with structural variants as input. It can match unnecessary huge amount of lines in annotation file and in such cases no CADD annotation will be made. See license. (plugin details)
default=0
example=snv_indels,1
@@ -2126,7 +2126,7 @@
type=Boolean
- description=Include CADD (Combined Annotation Dependent Depletion) deleteriousness scores for single nucleotide variants (also supports sus_scrofa and chicken (red jungle fowl)), indels and structural variants (only supported in GRCh38). Following options can be given: snv, indels, snv_indels, and sv. Providing 1 is also supported which is same as providing snv_indels. Caution to be taken while using snv, indels or snv_indels options with structural variants as input. It can match unnecessary huge amount of lines in annotation file and in such cases no CADD annotation will be made. See license. (plugin details)
+ description=Include CADD (Combined Annotation Dependent Depletion) deleteriousness scores for single nucleotide variants (also supports sus_scrofa, chicken (red jungle fowl) and turkey), indels and structural variants (only supported in GRCh38). Following options can be given: snv, indels, snv_indels, and sv. Providing 1 is also supported which is same as providing snv_indels. Caution to be taken while using snv, indels or snv_indels options with structural variants as input. It can match unnecessary huge amount of lines in annotation file and in such cases no CADD annotation will be made. See license. (plugin details)
default=0
example=snv_indels,1