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Turkey cadd e116 #933

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Merged
TamaraNaboulsi merged 5 commits into from
Feb 9, 2026
Merged

Turkey cadd e116 #933

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f5ae799
CADD for turkey
likhitha-surapaneni Sep 1, 2025
48f815f
Added combined file for cadd turkey
likhitha-surapaneni Sep 25, 2025
bd5bc07
File name change
likhitha-surapaneni Oct 8, 2025
2352fa9
Resolved conflicts
likhitha-surapaneni Jan 6, 2026
4d876be
Fix missing section
likhitha-surapaneni Jan 26, 2026
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8 changes: 8 additions & 0 deletions ensembl/conf/json/meleagris_gallopavo_vcf.json
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Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,14 @@
"type": "remote",
"filename_template": "/60_amniotes.gerp_conservation_score/gerp_conservation_scores.meleagris_gallopavo.Turkey_5.1.bw",
"annotation_type": "gerp"
},
{
"id": "CADD_Turkey_5.1_whole_genome_SNVs",
"species": "meleagris_gallopavo",
"assembly": "Turkey_5.1",
"type": "local",
"filename_template": "meleagris_gallopavo/Turkey_5.1/variant_annotation/tCADD.tsv.gz",
"annotation_type": "cadd"
}
]
}
2 changes: 1 addition & 1 deletion tools/modules/EnsEMBL/Web/Component/Tools/VEP/InputForm.pm
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Expand Up @@ -902,7 +902,7 @@ sub _build_predictions {
my $have_polyphen = first { $_->{'variation'}{'POLYPHEN'} } @$species;

if ($have_sift || $have_polyphen) {
my $fieldset = $form->add_fieldset({'legend' => $current_section, 'no_required_notes' => 1, 'class' => '_stt_pphn _stt_sift' });
my $fieldset = $form->add_fieldset({'legend' => $current_section, 'no_required_notes' => 1, 'class' => '_stt_pphn _stt_sift _stt_Meleagris_gallopavo' });

# sift
if ($have_sift) {
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7 changes: 7 additions & 0 deletions tools/modules/EnsEMBL/Web/Job/VEP.pm
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Expand Up @@ -242,6 +242,13 @@ sub _configure_plugins {
$param_aux =~ s/snv_chicken_rjf=//;
$param_clone = 'snv=' . $param_aux;
}
elsif($file_selected eq 'snv' && $job_data->{'species'} eq "Meleagris_gallopavo"){
next unless $param_clone =~ /^snv_turkey=/;

my $param_aux = $param_clone;
$param_aux =~ s/snv_turkey=//;
$param_clone = 'snv=' . $param_aux;
}
# Only add appropriate files based on selected option otherwise
elsif ($file_selected eq 'snv') {
next unless $param_clone =~ /^snv=/;
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1 change: 1 addition & 0 deletions tools_hive/conf/vep_plugins_hive_config.txt
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Expand Up @@ -39,6 +39,7 @@
"indels=[[ENSEMBL_VEP_PLUGIN_DATA_DIR]]/CADD_GRCh38_1.7_InDels.tsv.gz",
"snv_pig=[[ENSEMBL_VEP_PLUGIN_DATA_DIR]]/ALL_pCADD-PHRED-scores.tsv.gz",
"snv_chicken_rjf=[[ENSEMBL_VEP_PLUGIN_DATA_DIR]]/chCADD_updated.tsv.gz",
"snv_turkey=[[ENSEMBL_VEP_PLUGIN_DATA_DIR]]/tCADD.tsv.gz",
"sv=[[ENSEMBL_VEP_PLUGIN_DATA_DIR]]/CADD_prescored_variants.tsv.gz"
]
},
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