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Merged
TamaraNaboulsi merged 1 commit into from
Nov 25, 2025
Merged

Enable REST for turkey CADD - e116 #699

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11 changes: 11 additions & 0 deletions lib/EnsEMBL/REST/Controller/VEP.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -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=/;

Expand All @@ -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;
Expand Down
12 changes: 6 additions & 6 deletions root/documentation/vep.conf
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Original file line number Diff line number Diff line change
Expand Up @@ -312,7 +312,7 @@
</Phenotypes>
<CADD>
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: <b>snv</b>, <b>indels</b>, <b>snv_indels</b>, and <b>sv</b>. Providing 1 is also supported which is same as providing <b>snv_indels</b>. 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 <a target="_blank" href="https://cadd.gs.washington.edu/">license</a>. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/CADD.pm">plugin details</a>)
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: <b>snv</b>, <b>indels</b>, <b>snv_indels</b>, and <b>sv</b>. Providing 1 is also supported which is same as providing <b>snv_indels</b>. 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 <a target="_blank" href="https://cadd.gs.washington.edu/">license</a>. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/CADD.pm">plugin details</a>)
default=0
example=snv_indels,<wbr>1
</CADD>
Expand Down Expand Up @@ -682,7 +682,7 @@
</Phenotypes>
<CADD>
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: <b>snv</b>, <b>indels</b>, <b>snv_indels</b>, and <b>sv</b>. Providing 1 is also supported which is same as providing <b>snv_indels</b>. 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 <a target="_blank" href="https://cadd.gs.washington.edu/">license</a>. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/CADD.pm">plugin details</a>)
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: <b>snv</b>, <b>indels</b>, <b>snv_indels</b>, and <b>sv</b>. Providing 1 is also supported which is same as providing <b>snv_indels</b>. 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 <a target="_blank" href="https://cadd.gs.washington.edu/">license</a>. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/CADD.pm">plugin details</a>)
default=0
example=snv_indels,<wbr>1
</CADD>
Expand Down Expand Up @@ -1040,7 +1040,7 @@
</Phenotypes>
<CADD>
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: <b>snv</b>, <b>indels</b>, <b>snv_indels</b>, and <b>sv</b>. Providing 1 is also supported which is same as providing <b>snv_indels</b>. 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 <a target="_blank" href="https://cadd.gs.washington.edu/">license</a>. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/CADD.pm">plugin details</a>)
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: <b>snv</b>, <b>indels</b>, <b>snv_indels</b>, and <b>sv</b>. Providing 1 is also supported which is same as providing <b>snv_indels</b>. 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 <a target="_blank" href="https://cadd.gs.washington.edu/">license</a>. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/CADD.pm">plugin details</a>)
default=0
example=snv_indels,<wbr>1
</CADD>
Expand Down Expand Up @@ -1392,7 +1392,7 @@
</Phenotypes>
<CADD>
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: <b>snv</b>, <b>indels</b>, <b>snv_indels</b>, and <b>sv</b>. Providing 1 is also supported which is same as providing <b>snv_indels</b>. 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 <a target="_blank" href="https://cadd.gs.washington.edu/">license</a>. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/CADD.pm">plugin details</a>)
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: <b>snv</b>, <b>indels</b>, <b>snv_indels</b>, and <b>sv</b>. Providing 1 is also supported which is same as providing <b>snv_indels</b>. 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 <a target="_blank" href="https://cadd.gs.washington.edu/">license</a>. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/CADD.pm">plugin details</a>)
default=0
example=snv_indels,<wbr>1
</CADD>
Expand Down Expand Up @@ -1755,7 +1755,7 @@
</Phenotypes>
<CADD>
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: <b>snv</b>, <b>indels</b>, <b>snv_indels</b>, and <b>sv</b>. Providing 1 is also supported which is same as providing <b>snv_indels</b>. 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 <a target="_blank" href="https://cadd.gs.washington.edu/">license</a>. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/CADD.pm">plugin details</a>)
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: <b>snv</b>, <b>indels</b>, <b>snv_indels</b>, and <b>sv</b>. Providing 1 is also supported which is same as providing <b>snv_indels</b>. 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 <a target="_blank" href="https://cadd.gs.washington.edu/">license</a>. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/CADD.pm">plugin details</a>)
default=0
example=snv_indels,<wbr>1
</CADD>
Expand Down Expand Up @@ -2126,7 +2126,7 @@
</Phenotypes>
<CADD>
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: <b>snv</b>, <b>indels</b>, <b>snv_indels</b>, and <b>sv</b>. Providing 1 is also supported which is same as providing <b>snv_indels</b>. 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 <a target="_blank" href="https://cadd.gs.washington.edu/">license</a>. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/CADD.pm">plugin details</a>)
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: <b>snv</b>, <b>indels</b>, <b>snv_indels</b>, and <b>sv</b>. Providing 1 is also supported which is same as providing <b>snv_indels</b>. 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 <a target="_blank" href="https://cadd.gs.washington.edu/">license</a>. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/CADD.pm">plugin details</a>)
default=0
example=snv_indels,<wbr>1
</CADD>
Expand Down