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plugin_config.txt
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plugin_config.txt
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my $VEP_PLUGIN_CONFIG = {
"plugins" => [
## PATHOGENICITY PREDICTIONS
############################
# dbNSFP
# https://github.com/ensembl-variation/VEP_plugins/blob/main/dbNSFP.pm
# Requires tabix-indexed data file as first param
# Field names are listed below and rendered as a multi-selectable autocomplete text field
# Human, GRCh38 only (3.x), for GRCh37 use 2.9.x
{
"key" => "dbNSFP",
"label" => "dbNSFP",
"available" => 0,
"enabled" => 0,
"section" => "Pathogenicity predictions",
"helptip" => "dbNSFP provides pathogenicity predictions for missense variants from various algorithms",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/113/dbNSFP.pm",
"requires_data" => 1,
"requires_install" => 1,
"params" => [
#"/path/to/dbNSFP4.7c_grch38.gz",
"@*"
],
"species" => [
"homo_sapiens"
],
"form" => [
{
"name" => "dbNSFP_fields",
"label" => "Fields to include",
"helptip" => "Fields to fetch from dbNSFP; hold down the Ctrl (Windows) / Command (Mac) button to select multiple options",
"value" => "",
'type' => 'dropdown',
'multiple' => 1,
'style' => 'height:150px',
'required' => 1,
'notes' => 'Field descriptions in <a rel="external" href="https://usf.box.com/s/h9mqovab0on1r3hpopwypcjr9i9mf0s3">dbNSFP README</a>',
# "class" => "jquery-multiselect",
"values" => [
#"#chr",
#"pos(1-based)",
#"ref",
#"alt",
#"aaref",
#"aaalt",
#"rs_dbSNP",
#"hg19_chr",
#"hg19_pos(1-based)",
#"hg18_chr",
#"hg18_pos(1-based)",
"aapos",
"genename",
"Ensembl_geneid",
"Ensembl_transcriptid",
"Ensembl_proteinid",
"Uniprot_acc",
"Uniprot_entry",
#"HGVSc_ANNOVAR",
#"HGVSp_ANNOVAR",
#"HGVSc_snpEff",
#"HGVSp_snpEff",
#"HGVSc_VEP",
#"HGVSp_VEP",
#"APPRIS",
#"GENCODE_basic",
#"TSL",
#"VEP_canonical",
#"cds_strand",
#"refcodon",
#"codonpos",
"codon_degeneracy",
"Ancestral_allele",
"AltaiNeandertal",
"Denisova",
"VindijiaNeandertal",
"ChagyrskayaNeandertal",
#"SIFT_score",
#"SIFT_converted_rankscore",
#"SIFT_pred",
#"SIFT4G_score",
#"SIFT4G_converted_rankscore",
#"SIFT4G_pred",
"LRT_score",
"LRT_converted_rankscore",
"LRT_pred",
"LRT_Omega",
"MutationTaster_score",
"MutationTaster_converted_rankscore",
"MutationTaster_pred",
"MutationTaster_model",
"MutationTaster_AAE",
"MutationAssessor_score",
"MutationAssessor_rankscore",
"MutationAssessor_pred",
"FATHMM_score",
"FATHMM_converted_rankscore",
"FATHMM_pred",
"PROVEAN_score",
"PROVEAN_converted_rankscore",
"PROVEAN_pred",
"MetaSVM_score",
"MetaSVM_rankscore",
"MetaSVM_pred",
"MetaLR_score",
"MetaLR_rankscore",
"MetaLR_pred",
"Reliability_index",
"MetaRNN_score",
"MetaRNN_rankscore",
"MetaRNN_pred",
"M-CAP_score",
"M-CAP_rankscore",
"M-CAP_pred",
"MutPred_score",
"MutPred_rankscore",
"MutPred_protID",
"MutPred_AAchange",
"MutPred_Top5features",
"MVP_score",
"MVP_rankscore",
"gMVP_score",
"gMVP_rankscore",
"MPC_score",
"MPC_rankscore",
"PrimateAI_score",
"PrimateAI_rankscore",
"PrimateAI_pred",
"DEOGEN2_score",
"DEOGEN2_rankscore",
"DEOGEN2_pred",
"BayesDel_addAF_score",
"BayesDel_addAF_rankscore",
"BayesDel_addAF_pred",
"BayesDel_noAF_score",
"BayesDel_noAF_rankscore",
"BayesDel_noAF_pred",
"LIST-S2_score",
"LIST-S2_rankscore",
"LIST-S2_pred",
"VARITY_R_score",
"VARITY_R_rankscore",
"VARITY_ER_score",
"VARITY_ER_rankscore",
"VARITY_R_LOO_score",
"VARITY_R_LOO_rankscore",
"VARITY_ER_LOO_score",
"VARITY_ER_LOO_rankscore",
"ESM1b_score",
"ESM1b_rankscore",
"ESM1b_pred",
"EVE_score",
"EVE_rankscore",
"EVE_Class10_pred",
"EVE_Class20_pred",
"EVE_Class25_pred",
"EVE_Class30_pred",
"EVE_Class40_pred",
"EVE_Class50_pred",
"EVE_Class60_pred",
"EVE_Class70_pred",
"EVE_Class75_pred",
"EVE_Class80_pred",
"EVE_Class90_pred",
"Aloft_Fraction_transcripts_affected",
"Aloft_prob_Tolerant",
"Aloft_prob_Recessive",
"Aloft_prob_Dominant",
"Aloft_pred",
"Aloft_Confidence",
"DANN_score",
"DANN_rankscore",
"fathmm-MKL_coding_score",
"fathmm-MKL_coding_rankscore",
"fathmm-MKL_coding_pred",
"fathmm-MKL_coding_group",
"fathmm-XF_coding_score",
"fathmm-XF_coding_rankscore",
"fathmm-XF_coding_pred",
"Eigen-raw_coding",
"Eigen-raw_coding_rankscore",
"Eigen-phred_coding",
"Eigen-PC-raw_coding",
"Eigen-PC-raw_coding_rankscore",
"Eigen-PC-phred_coding",
"integrated_fitCons_score",
"integrated_fitCons_rankscore",
"integrated_confidence_value",
"GM12878_fitCons_score",
"GM12878_fitCons_rankscore",
"GM12878_confidence_value",
"H1-hESC_fitCons_score",
"H1-hESC_fitCons_rankscore",
"H1-hESC_confidence_value",
"HUVEC_fitCons_score",
"HUVEC_fitCons_rankscore",
"HUVEC_confidence_value",
"GERP++_NR",
"GERP++_RS",
"GERP++_RS_rankscore",
"phyloP100way_vertebrate",
"phyloP100way_vertebrate_rankscore",
"phyloP470way_mammalian",
"phyloP470way_mammalian_rankscore",
"phyloP17way_primate",
"phyloP17way_primate_rankscore",
"phastCons100way_vertebrate",
"phastCons100way_vertebrate_rankscore",
"phastCons470way_mammalian",
"phastCons470way_mammalian_rankscore",
"phastCons17way_primate",
"phastCons17way_primate_rankscore",
"SiPhy_29way_pi",
"SiPhy_29way_logOdds",
"SiPhy_29way_logOdds_rankscore",
"bStatistic",
"bStatistic_converted_rankscore",
"1000Gp3_AC",
"1000Gp3_AF",
"1000Gp3_AFR_AC",
"1000Gp3_AFR_AF",
"1000Gp3_EUR_AC",
"1000Gp3_EUR_AF",
"1000Gp3_AMR_AC",
"1000Gp3_AMR_AF",
"1000Gp3_EAS_AC",
"1000Gp3_EAS_AF",
"1000Gp3_SAS_AC",
"1000Gp3_SAS_AF",
"TWINSUK_AC",
"TWINSUK_AF",
"ALSPAC_AC",
"ALSPAC_AF",
"UK10K_AC",
"UK10K_AF",
"ESP6500_AA_AC",
"ESP6500_AA_AF",
"ESP6500_EA_AC",
"ESP6500_EA_AF",
"ExAC_AC",
"ExAC_AF",
"ExAC_Adj_AC",
"ExAC_Adj_AF",
"ExAC_AFR_AC",
"ExAC_AFR_AF",
"ExAC_AMR_AC",
"ExAC_AMR_AF",
"ExAC_EAS_AC",
"ExAC_EAS_AF",
"ExAC_FIN_AC",
"ExAC_FIN_AF",
"ExAC_NFE_AC",
"ExAC_NFE_AF",
"ExAC_SAS_AC",
"ExAC_SAS_AF",
"ExAC_nonTCGA_AC",
"ExAC_nonTCGA_AF",
"ExAC_nonTCGA_Adj_AC",
"ExAC_nonTCGA_Adj_AF",
"ExAC_nonTCGA_AFR_AC",
"ExAC_nonTCGA_AFR_AF",
"ExAC_nonTCGA_AMR_AC",
"ExAC_nonTCGA_AMR_AF",
"ExAC_nonTCGA_EAS_AC",
"ExAC_nonTCGA_EAS_AF",
"ExAC_nonTCGA_FIN_AC",
"ExAC_nonTCGA_FIN_AF",
"ExAC_nonTCGA_NFE_AC",
"ExAC_nonTCGA_NFE_AF",
"ExAC_nonTCGA_SAS_AC",
"ExAC_nonTCGA_SAS_AF",
"ExAC_nonpsych_AC",
"ExAC_nonpsych_AF",
"ExAC_nonpsych_Adj_AC",
"ExAC_nonpsych_Adj_AF",
"ExAC_nonpsych_AFR_AC",
"ExAC_nonpsych_AFR_AF",
"ExAC_nonpsych_AMR_AC",
"ExAC_nonpsych_AMR_AF",
"ExAC_nonpsych_EAS_AC",
"ExAC_nonpsych_EAS_AF",
"ExAC_nonpsych_FIN_AC",
"ExAC_nonpsych_FIN_AF",
"ExAC_nonpsych_NFE_AC",
"ExAC_nonpsych_NFE_AF",
"ExAC_nonpsych_SAS_AC",
"ExAC_nonpsych_SAS_AF",
"gnomAD_exomes_flag",
"gnomAD_exomes_AC",
"gnomAD_exomes_AN",
"gnomAD_exomes_AF",
"gnomAD_exomes_nhomalt",
"gnomAD_exomes_POPMAX_AC",
"gnomAD_exomes_POPMAX_AN",
"gnomAD_exomes_POPMAX_AF",
"gnomAD_exomes_POPMAX_nhomalt",
"gnomAD_exomes_AFR_AC",
"gnomAD_exomes_AFR_AN",
"gnomAD_exomes_AFR_AF",
"gnomAD_exomes_AFR_nhomalt",
"gnomAD_exomes_AMR_AC",
"gnomAD_exomes_AMR_AN",
"gnomAD_exomes_AMR_AF",
"gnomAD_exomes_AMR_nhomalt",
"gnomAD_exomes_ASJ_AC",
"gnomAD_exomes_ASJ_AN",
"gnomAD_exomes_ASJ_AF",
"gnomAD_exomes_ASJ_nhomalt",
"gnomAD_exomes_EAS_AC",
"gnomAD_exomes_EAS_AN",
"gnomAD_exomes_EAS_AF",
"gnomAD_exomes_EAS_nhomalt",
"gnomAD_exomes_FIN_AC",
"gnomAD_exomes_FIN_AN",
"gnomAD_exomes_FIN_AF",
"gnomAD_exomes_FIN_nhomalt",
"gnomAD_exomes_MID_AC",
"gnomAD_exomes_MID_AN",
"gnomAD_exomes_MID_AF",
"gnomAD_exomes_MID_nhomalt",
"gnomAD_exomes_NFE_AC",
"gnomAD_exomes_NFE_AN",
"gnomAD_exomes_NFE_AF",
"gnomAD_exomes_NFE_nhomalt",
"gnomAD_exomes_SAS_AC",
"gnomAD_exomes_SAS_AN",
"gnomAD_exomes_SAS_AF",
"gnomAD_exomes_SAS_nhomalt",
"gnomAD_exomes_non_ukb_AC",
"gnomAD_exomes_non_ukb_AN",
"gnomAD_exomes_non_ukb_AF",
"gnomAD_exomes_non_ukb_nhomalt",
"gnomAD_exomes_non_ukb_AFR_AC",
"gnomAD_exomes_non_ukb_AFR_AN",
"gnomAD_exomes_non_ukb_AFR_AF",
"gnomAD_exomes_non_ukb_AFR_nhomalt",
"gnomAD_exomes_non_ukb_AMR_AC",
"gnomAD_exomes_non_ukb_AMR_AN",
"gnomAD_exomes_non_ukb_AMR_AF",
"gnomAD_exomes_non_ukb_AMR_nhomalt",
"gnomAD_exomes_non_ukb_ASJ_AC",
"gnomAD_exomes_non_ukb_ASJ_AN",
"gnomAD_exomes_non_ukb_ASJ_AF",
"gnomAD_exomes_non_ukb_ASJ_nhomalt",
"gnomAD_exomes_non_ukb_EAS_AC",
"gnomAD_exomes_non_ukb_EAS_AN",
"gnomAD_exomes_non_ukb_EAS_AF",
"gnomAD_exomes_non_ukb_EAS_nhomalt",
"gnomAD_exomes_non_ukb_FIN_AC",
"gnomAD_exomes_non_ukb_FIN_AN",
"gnomAD_exomes_non_ukb_FIN_AF",
"gnomAD_exomes_non_ukb_FIN_nhomalt",
"gnomAD_exomes_non_ukb_MID_AC",
"gnomAD_exomes_non_ukb_MID_AN",
"gnomAD_exomes_non_ukb_MID_AF",
"gnomAD_exomes_non_ukb_MID_nhomalt",
"gnomAD_exomes_non_ukb_NFE_AC",
"gnomAD_exomes_non_ukb_NFE_AN",
"gnomAD_exomes_non_ukb_NFE_AF",
"gnomAD_exomes_non_ukb_NFE_nhomalt",
"gnomAD_exomes_non_ukb_SAS_AC",
"gnomAD_exomes_non_ukb_SAS_AN",
"gnomAD_exomes_non_ukb_SAS_AF",
"gnomAD_exomes_non_ukb_SAS_nhomalt",
"gnomAD_genomes_flag",
"gnomAD_genomes_AC",
"gnomAD_genomes_AN",
"gnomAD_genomes_AF",
"gnomAD_genomes_nhomalt",
"gnomAD_genomes_POPMAX_AC",
"gnomAD_genomes_POPMAX_AN",
"gnomAD_genomes_POPMAX_AF",
"gnomAD_genomes_POPMAX_nhomalt",
"gnomAD_genomes_AFR_AC",
"gnomAD_genomes_AFR_AN",
"gnomAD_genomes_AFR_AF",
"gnomAD_genomes_AFR_nhomalt",
"gnomAD_genomes_AMI_AC",
"gnomAD_genomes_AMI_AN",
"gnomAD_genomes_AMI_AF",
"gnomAD_genomes_AMI_nhomalt",
"gnomAD_genomes_AMR_AC",
"gnomAD_genomes_AMR_AN",
"gnomAD_genomes_AMR_AF",
"gnomAD_genomes_AMR_nhomalt",
"gnomAD_genomes_ASJ_AC",
"gnomAD_genomes_ASJ_AN",
"gnomAD_genomes_ASJ_AF",
"gnomAD_genomes_ASJ_nhomalt",
"gnomAD_genomes_EAS_AC",
"gnomAD_genomes_EAS_AN",
"gnomAD_genomes_EAS_AF",
"gnomAD_genomes_EAS_nhomalt",
"gnomAD_genomes_FIN_AC",
"gnomAD_genomes_FIN_AN",
"gnomAD_genomes_FIN_AF",
"gnomAD_genomes_FIN_nhomalt",
"gnomAD_genomes_MID_AC",
"gnomAD_genomes_MID_AN",
"gnomAD_genomes_MID_AF",
"gnomAD_genomes_MID_nhomalt",
"gnomAD_genomes_NFE_AC",
"gnomAD_genomes_NFE_AN",
"gnomAD_genomes_NFE_AF",
"gnomAD_genomes_NFE_nhomalt",
"gnomAD_genomes_SAS_AC",
"gnomAD_genomes_SAS_AN",
"gnomAD_genomes_SAS_AF",
"gnomAD_genomes_SAS_nhomalt",
"ALFA_European_AC",
"ALFA_European_AN",
"ALFA_European_AF",
"ALFA_African_Others_AC",
"ALFA_African_Others_AN",
"ALFA_African_Others_AF",
"ALFA_East_Asian_AC",
"ALFA_East_Asian_AN",
"ALFA_East_Asian_AF",
"ALFA_African_American_AC",
"ALFA_African_American_AN",
"ALFA_African_American_AF",
"ALFA_Latin_American_1_AC",
"ALFA_Latin_American_1_AN",
"ALFA_Latin_American_1_AF",
"ALFA_Latin_American_2_AC",
"ALFA_Latin_American_2_AN",
"ALFA_Latin_American_2_AF",
"ALFA_Other_Asian_AC",
"ALFA_Other_Asian_AN",
"ALFA_Other_Asian_AF",
"ALFA_South_Asian_AC",
"ALFA_South_Asian_AN",
"ALFA_South_Asian_AF",
"ALFA_Other_AC",
"ALFA_Other_AN",
"ALFA_Other_AF",
"ALFA_African_AC",
"ALFA_African_AN",
"ALFA_African_AF",
"ALFA_Asian_AC",
"ALFA_Asian_AN",
"ALFA_Asian_AF",
"ALFA_Total_AC",
"ALFA_Total_AN",
"ALFA_Total_AF",
"clinvar_id",
"clinvar_clnsig",
"clinvar_trait",
"clinvar_review",
"clinvar_hgvs",
"clinvar_var_source",
"clinvar_MedGen_id",
"clinvar_OMIM_id",
"clinvar_Orphanet_id",
"Interpro_domain",
"GTEx_V8_eQTL_gene",
"GTEx_V8_eQTL_tissue",
"GTEx_V8_sQTL_gene",
"GTEx_V8_sQTL_tissue",
"eQTLGen_snp_id",
"eQTLGen_gene_id",
"eQTLGen_gene_symbol",
"eQTLGen_cis_or_trans",
"Geuvadis_eQTL_target_gene",
],
},
{
"name" => "dbNSFP_transcript_match",
"label" => "Transcript match",
"helptip" => "By default, some dbNSFP fields contain values for all Ensembl transcripts. Select this to only return values for the matched Ensembl transcript.",
"value" => "transcript_match=1",
"type" => "checkbox",
"style" => "height:150px"
}
]
},
# AlphaMissense
{
"key" => "AlphaMissense",
"label" => "AlphaMissense",
"available" => 0,
"enabled" => 0,
"section" => "Pathogenicity predictions",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/113/AlphaMissense.pm",
"helptip" => "Annotates missense variants with the pre-computed AlphaMissense pathogenicity scores. AlphaMissense is a deep learning model developed by Google DeepMind that predicts the pathogenicity of single nucleotide missense variants.",
"requires_data" => 1,
"species" => [
"homo_sapiens"
],
"params" => [
#"file=/path/to/AlphaMissense_hg38.tsv.gz"
]
},
# AVADA
{
"key" => "AVADA",
"label" => "AVADA",
"available" => 0,
"enabled" => 0,
"section" => "Phenotype data and citations",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/113/AVADA.pm",
},
# CADD
# https://github.com/ensembl-variation/VEP_plugins/blob/main/CADD.pm
{
"key" => "CADD",
"label" => "CADD",
"available" => 0,
"enabled" => 0,
"section" => "Pathogenicity predictions",
"helptip" => "Combined Annotation Dependent Depletion (CADD) is a tool for scoring the deleteriousness of single nucleotide variants and insertion/deletion variants in the human genome. CADD integrates multiple annotations into one metric by contrasting variants that survived natural selection with simulated mutations. CADD is only available here for non-commercial use. See CADD website for more information.",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/113/CADD.pm",
"requires_data" => 1,
"species" => [
"homo_sapiens",
"sus_scrofa"
],
"form" => [
{
"name" => "file_type",
"label" => "Select annotation file",
"type" => "dropdown",
"helptip" => "Select type of CADD annotation file to be used. 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.",
"values" => [
{ "value" => "snv_indels", "caption" => "CADD SNVs and InDels annotation file", "class" => "_stt_Homo_sapiens" },
{ "value" => "snv", "caption" => "CADD SNVs annotation file" },
{ "value" => "indels", "caption" => "CADD InDels annotation file", "class" => "_stt_Homo_sapiens" },
{ "value" => "sv", "caption" => "CADD-SV annotation file (supported only in GRCh38)", "class" => "_stt_Homo_sapiens" }
],
"value" => "snv_indels",
},
],
"params" => [
#"snv=/path/to/CADD_whole_genome_SNVs.tsv.gz",
#"indels=/path/to/CADD_GRCh38_1.6_InDels.tsv.gz",
#"snv_pig=/path/to/ALL_pCADD-PHRED-scores.tsv.gz",
#"sv=/path/to/CADD_prescored_variants.tsv.gz"
]
},
# CAPICE
# https://github.com/ensembl-variation/VEP_plugins/blob/main/CAPICE.pm
# Requires tabix-indexed data files as params (one for InDels, another for SNVs)
# No other parameters so no form required
# data file currently only available for GRCh37
{
"key" => "CAPICE",
"label" => "CAPICE",
"available" => 0,
"enabled" => 0,
"section" => "Pathogenicity predictions",
"helptip" => "Consequence-Agnostic Pathogenicity Interpretation of Clinical Exome variations (CAPICE) is a tool for scoring the pathogenicity of single nucleotide variants and insertion/deletion variants in the human genome. CAPICE uses a gradient boosting tree model trained with multiple genomic annotations used by CADD score and based on clinical significance.",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/113/CAPICE.pm",
"requires_data" => 1,
"species" => [
"homo_sapiens"
],
"params" => [
#"/path/to/capice_v1.0_build37_indels.tsv.gz",
#"/path/to/capice_v1.0_build37_snvs.tsv.gz"
]
},
# FATHMM
{
"key" => "FATHMM",
"label" => "FATHMM",
"available" => 0,
"enabled" => 0,
"section" => "Pathogenicity predictions",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/113/FATHMM.pm"
},
# FATHMM-MKL
# https://github.com/ensembl-variation/VEP_plugins/blob/main/FATHMM_MKL.pm
# Requires tabix-indexed data file as first param
# No other parameters so no form required
# data file currently only available for GRCh37
{
"key" => "FATHMM_MKL",
"label" => "FATHMM-MKL",
"available" => 0,
"enabled" => 0,
"section" => "Pathogenicity predictions",
"helptip" => "FATHMM-MKL predicts functional consequences of variants, both coding and non-coding.",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/113/FATHMM_MKL.pm",
"requires_data" => 1,
"species" => [
"homo_sapiens"
],
"params" => [
#"/path/to/fathmm-MKL_Current.tab.gz"
]
},
# GWAVA
# https://www.sanger.ac.uk/sanger/StatGen_Gwava
# Requires tabix-indexed BED data file from ftp://ftp.sanger.ac.uk/pub/resources/software/gwava/v1.0/VEP_plugin/
# data file currently only available for GRCh37
{
"key" => "Gwava",
"label" => "GWAVA",
"available" => 0,
"enabled" => 0,
"section" => "Pathogenicity predictions",
"helptip" => "Retrieves precomputed Genome Wide Annotation of VAriants (GWAVA) scores for any variant that overlaps a known variant from the Ensembl variation database",
"plugin_url" => "ftp://ftp.sanger.ac.uk/pub/resources/software/gwava/v1.0/VEP_plugin/Gwava.pm",
"requires_data" => 1,
"species" => [
"homo_sapiens"
],
"params" => [
"@*",
# "/path/to/gwava_scores.bed.gz"
],
"form" => [
{
"name" => "model",
"label" => "Model",
"type" => "dropdown",
"values" => [
{ "value" => "region", "caption" => "Region" },
{ "value" => "tss", "caption" => "TSS" },
{ "value" => "unmatched", "caption" => "Unmatched" }
],
"value" => "region",
},
],
},
# Carol
# https://github.com/ensembl-variation/VEP_plugins/blob/main/Carol.pm
# Requires Math/CDF Perl module
{
"key" => "Carol",
"helptip" => "Calculates the Combined Annotation scoRing toOL (CAROL) score for a missense mutation based on the pre-calculated SIFT and PolyPhen scores",
"available" => 0,
"enabled" => 0,
"section" => "Pathogenicity predictions",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/113/Carol.pm",
"requires_install" => 1,
"species" => [
"homo_sapiens"
],
},
# Condel
# https://github.com/ensembl-variation/VEP_plugins/blob/main/Condel.pm
# Requires path to config directory as first param
# config directory is checked out as part of VEP_plugins repo, as /[path]/VEP_plugins/config/Condel/config
# Within that dir, edit condel_SP.conf so that condel.dir points to /[path]/VEP_plugins/config/Condel
{
"key" => "Condel",
"helptip" => "Calculates the Consensus Deleteriousness (Condel) score for a missense mutation based on the pre-calculated SIFT and PolyPhen scores",
"available" => 0,
"enabled" => 0,
"section" => "Pathogenicity predictions",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/113/Condel.pm",
"requires_install" => 1,
"species" => [
"homo_sapiens"
],
"params" => [
# "/path/to/config/Condel/config",
"@*"
],
"form" => [
{
"name" => "score_pred",
"label" => "Score/prediction",
"type" => "dropdown",
"values" => [
{ "value" => "b", "caption" => "Prediction and score" },
{ "value" => "p", "caption" => "Prediction only" },
{ "value" => "s", "caption" => "Score only" }
],
"value" => "b",
},
],
},
# LOFTEE
# See https://github.com/konradjk/loftee for details
{
"key" => "LoF",
"helptip" => "LOFTEE identifies LoF (loss-of-function) variation",
"available" => 0,
"enabled" => 0,
"section" => "Pathogenicity predictions",
"plugin_url" => "https://raw.githubusercontent.com/konradjk/loftee/master/LoF.pm",
"requires_data" => 1,
"requires_install" => 1,
"params" => [
"@*"
]
},
# LoFtool
# Requires LoFtool_scores.txt file as first param (available in VEP_plugins GitHub repo)
{
"key" => "LoFtool",
"helptip" => "Provides a per-gene rank of genic intolerance and consequent susceptibility to disease based on the ratio of Loss-of-function (LoF) to synonymous mutations in ExAC data",
"available" => 0,
"enabled" => 0,
"section" => "Pathogenicity predictions",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/113/LoFtool.pm",
"requires_data" => 1,
"species" => [
"homo_sapiens"
],
"params" => [
# "/path/to/LoFtool_scores.txt"
]
},
# MPC
# Requires fordist_constraint_official_mpc_values.txt.gz data file
{
"key" => "MPC",
"helptip" => "MPC is a missense deleteriousness metric based on the analysis of genic regions depleted of missense mutations in ExAC",
"available" => 0,
"enabled" => 0,
"section" => "Pathogenicity predictions",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/113/MPC.pm",
"requires_data" => 1,
"species" => [
"homo_sapiens"
],
"params" => [
# "/path/to/fordist_constraint_official_mpc_values.txt.gz"
]
},
# MTR
# Requires mtrflatfile_1.0.txt.gz data file from ftp://mtr-viewer.mdhs.unimelb.edu.au/pub
{
"key" => "MTR",
"helptip" => "MTR scores quantify the amount of purifying selection acting specifically on missense variants in a given window of protein-coding sequence",
"available" => 0,
"enabled" => 0,
"section" => "Pathogenicity predictions",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/113/MTR.pm",
"requires_data" => 1,
"species" => [
"homo_sapiens"
],
"params" => [
# "/path/to/mtrflatfile_1.0.txt.gz"
]
},
# PrimateAI
# Requires PrimateAI_scores_v0.2.tsv.gz or PrimateAI_scores_v0.2_hg38.tsv.gz from https://basespace.illumina.com/s/yYGFdGih1rXL.
{
"key" => "PrimateAI",
"helptip" => "PrimateAI scores can be used to assess pathogenicity of variants in humans",
"available" => 0,
"enabled" => 0,
"section" => "Pathogenicity predictions",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/113/PrimateAI.pm",
"requires_data" => 1,
"species" => [
"homo_sapiens"
],
"params" => [
# "/path/to/PrimateAI_scores_v0.2_GRCh38_sorted.tsv.bgz
]
},
# REVEL
# Requires data file processed from revel_all_chromosomes.csv.zip
{
"key" => "REVEL",
"helptip" => "An ensemble method for predicting the pathogenicity of rare missense variants",
"available" => 0,
"enabled" => 0,
"section" => "Pathogenicity predictions",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/113/REVEL.pm",
"requires_data" => 1,
"species" => [
"homo_sapiens"
],
"params" => [
# "/path/to/revel_all_chromosomes.tsv.gz"
]
},
# PON_P2
{
"key" => "PON_P2",
"label" => "PON_P2",
"available" => 0,
"enabled" => 0,
"section" => "Pathogenicity predictions",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/113/PON_P2.pm"
},
# ClinPred
# Requires data file processed from ClinPred.txt.gz
{
"key" => "ClinPred",
"helptip" => "A prediction tool for the identification of disease-relevant nonsynonymous single nucleotide variants",
"available" => 0,
"enabled" => 0,
"section" => "Pathogenicity predictions",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/113/ClinPred.pm",
"requires_data" => 1,
"species" => [
"homo_sapiens"
],
"params" => [
# "/path/to/ClinPred_tabbed.tsv.gz"
]
},
# EVE
# https://github.com/ensembl-variation/VEP_plugins/blob/main/EVE.pm
# Requires tabix-indexed data file as params
# No other parameters so no form required
# data file currently only available for GRCh38
# We only report EVE scores for input variants and
# don't consider adjacent variants.
{
"key" => "EVE",
"label" => "EVE",
"available" => 0,
"enabled" => 0,
"section" => "Pathogenicity predictions",
"helptip" => "EVE (evolutionary model of variant effect) is a computational method for the classification of human genetic variants trained solely on evolutionary sequences.",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/113/EVE.pm",
"requires_data" => 1,
"species" => [
"homo_sapiens"
],
"params" => [
#"/path/to/eve_merged.vcf.gz"
]
},
# Paralogues
{
"key" => "Paralogues",
"label" => "Paralogue variants",
"available" => 0,
"enabled" => 0,
"section" => "Variant data",
"helptip" => "Retrieves ClinVar variants that overlap genomic coordinates corresponding to aligned amino acid positions in paralogous proteins",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/113/Paralogues.pm",
"requires_data" => 1,
"species" => [
"homo_sapiens"
],
"params" => [
#"matches=/path/to/paralogues_matches.tsv.gz",
"@*"
],
"form" => [
{
"name" => "clnsig",
"label" => "Clinical significance",
"helptip" => "Clinical significance term used to filter paralogue variants",
"type" => "dropdown",
"values" => [
{ "value" => "clnsig=pathogenic", "caption" => "Pathogenic" },
{ "value" => "clnsig=benign", "caption" => "Benign" },
{ "value" => "clnsig=uncertain_significance", "caption" => "Uncertain significance" },
{ "value" => "clnsig=ignore", "caption" => "Ignore (fetch all paralogue variants)" }
],
"value" => "clnsig=pathogenic"
},
{
"name" => "clnsig_match",
"label" => "Clinical significance match type",
"helptip" => "Type of match when filtering paralogue variants based on clinical significance (e.g., using 'Pathogenic' and 'Partial match' will fetch variants that are pathogenic and likely pathogenic, whereas 'Exact match' will only fetch pathogenic variants)",
"type" => "dropdown",
"values" => [
{ "value" => "clnsig_match=partial", "caption" => "Partial match" },
{ "value" => "clnsig_match=exact", "caption" => "Exact match" }
],
"value" => "clnsig_match=partial"
}
]
},
# BayesDel
{
"key" => "BayesDel",
"label" => "BayesDel",
"available" => 0,
"enabled" => 0,
"section" => "Pathogenicity predictions",
"helptip" => "BayesDel adds a deleteriousness meta-score combining multiple deleteriousness predictors.",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/113/BayesDel.pm",
"requires_data" => 1,
"species" => [
"homo_sapiens"
],
"params" => [
#"/path/to/BayesDel.vcf.gz"
]
},
# PolyPhen_SIFT
{
"key" => "PolyPhen_SIFT",
"available" => 0,
"enabled" => 0,
"section" => "Pathogenicity predictions",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/113/PolyPhen_SIFT.pm",
},
## SPLICING PREDICTIONS
#######################
# dbscSNV
{
"key" => "dbscSNV",
"label" => "dbscSNV",
"available" => 0,
"enabled" => 0,
"section" => "Splicing predictions",
"helptip" => "Retrieves data for splicing variants from a tabix-indexed dbscSNV file",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/113/dbscSNV.pm",
"requires_data" => 1,
"requires_install" => 1,
"params" => [
#"/path/to/dbscSNV1.1.txt.gz"
],
"species" => [
"homo_sapiens"
],
},
# GeneSplicer
{
"key" => "GeneSplicer",
"label" => "GeneSplicer",
"helptip" => "Detects splice sites in genomic DNA",
"available" => 0,
"enabled" => 0,
"section" => "Splicing predictions",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/113/GeneSplicer.pm",
"requires_install" => 1,
"species" => [
"homo_sapiens"
],
"params" => [
#"/path/to/genesplicer/bin/linux/genesplicer",
#"/path/to/genesplicer/human",
"@*"
]
},
# MaxEntScan
{
"key" => "MaxEntScan",
"label" => "MaxEntScan",
"helptip" => "Sequence motif and maximum entropy based splice site consensus predictions",
"available" => 0,
"enabled" => 0,
"section" => "Splicing predictions",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/113/MaxEntScan.pm",
"requires_install" => 1,
"species" => [
"homo_sapiens"
],
"params" => [
#"/path/to/maxentscan"
]
},
# SpliceRegion
{
"key" => "SpliceRegion",
"label" => "SpliceRegion",
"helptip" => "More granular predictions of splicing effects",
"available" => 0,
"enabled" => 0,
"section" => "Splicing predictions",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/113/SpliceRegion.pm",
},
# SpliceAI
{
"key" => "SpliceAI",
"label" => "SpliceAI",
"helptip" => "Pre-calculated annotations from SpliceAI a deep neural network, developed by Illumina, Inc that predicts splice junctions from an arbitrary pre-mRNA transcript sequence. Used for non-commercial purposes (https://github.com/Illumina/SpliceAI)",
"available" => 0,
"enabled" => 0,
"section" => "Splicing predictions",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/113/SpliceAI.pm",
"species" => [
"homo_sapiens"
],
"form" => [
{