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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/master/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/102/dbNSFP.pm",
"requires_data" => 1,
"requires_install" => 1,
"params" => [
#"/path/to/dbNSFP4.1a_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://drive.google.com/file/d/1VINShZQYN63HvigJA_SiuOYIk8TWl5Fh/view">dbNSFP README</a>',
# "class" => "jquery-multiselect",
"values" => [
#"#chr",
#"pos(1-based)",
#"ref",
#"alt",
#"aaref",
#"aaalt",
#"rs_dbSNP151",
#"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",
#"SIFT_score",
#"SIFT_converted_rankscore",
#"SIFT_pred",
#"SIFT4G_score",
#"SIFT4G_converted_rankscore",
#"SIFT4G_pred",
#"Polyphen2_HDIV_score",
#"Polyphen2_HDIV_rankscore",
#"Polyphen2_HDIV_pred",
#"Polyphen2_HVAR_score",
#"Polyphen2_HVAR_rankscore",
#"Polyphen2_HVAR_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",
"VEST4_score",
"VEST4_rankscore",
"MetaSVM_score",
"MetaSVM_rankscore",
"MetaSVM_pred",
"MetaLR_score",
"MetaLR_rankscore",
"MetaLR_pred",
"Reliability_index",
"M-CAP_score",
"M-CAP_rankscore",
"M-CAP_pred",
"REVEL_score",
"REVEL_rankscore",
"MutPred_score",
"MutPred_rankscore",
"MutPred_protID",
"MutPred_AAchange",
"MutPred_Top5features",
"MVP_score",
"MVP_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",
"ClinPred_score",
"ClinPred_rankscore",
"ClinPred_pred",
"LIST-S2_score",
"LIST-S2_rankscore",
"LIST-S2_pred",
"Aloft_Fraction_transcripts_affected",
"Aloft_prob_Tolerant",
"Aloft_prob_Recessive",
"Aloft_prob_Dominant",
"Aloft_pred",
"Aloft_Confidence",
"CADD_raw",
"CADD_raw_rankscore",
"CADD_phred",
"CADD_raw_hg19",
"CADD_raw_rankscore_hg19",
"CADD_phred_hg19",
"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",
"GenoCanyon_score",
"GenoCanyon_rankscore",
"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",
"LINSIGHT",
"LINSIGHT_rankscore",
"GERP++_NR",
"GERP++_RS",
"GERP++_RS_rankscore",
"phyloP100way_vertebrate",
"phyloP100way_vertebrate_rankscore",
"phyloP30way_mammalian",
"phyloP30way_mammalian_rankscore",
"phyloP17way_primate",
"phyloP17way_primate_rankscore",
"phastCons100way_vertebrate",
"phastCons100way_vertebrate_rankscore",
"phastCons30way_mammalian",
"phastCons30way_mammalian_rankscore",
"phastCons17way_primate",
"phastCons17way_primate_rankscore",
"SiPhy_29way_pi",
"SiPhy_29way_logOdds",
"SiPhy_29way_logOdds_rankscore",
"bStatistic",
"bStatistic_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_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_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_POPMAX_AC",
"gnomAD_exomes_POPMAX_AN",
"gnomAD_exomes_POPMAX_AF",
"gnomAD_exomes_POPMAX_nhomalt",
"gnomAD_exomes_controls_AC",
"gnomAD_exomes_controls_AN",
"gnomAD_exomes_controls_AF",
"gnomAD_exomes_controls_nhomalt",
"gnomAD_exomes_controls_AFR_AC",
"gnomAD_exomes_controls_AFR_AN",
"gnomAD_exomes_controls_AFR_AF",
"gnomAD_exomes_controls_AFR_nhomalt",
"gnomAD_exomes_controls_AMR_AC",
"gnomAD_exomes_controls_AMR_AN",
"gnomAD_exomes_controls_AMR_AF",
"gnomAD_exomes_controls_AMR_nhomalt",
"gnomAD_exomes_controls_ASJ_AC",
"gnomAD_exomes_controls_ASJ_AN",
"gnomAD_exomes_controls_ASJ_AF",
"gnomAD_exomes_controls_ASJ_nhomalt",
"gnomAD_exomes_controls_EAS_AC",
"gnomAD_exomes_controls_EAS_AN",
"gnomAD_exomes_controls_EAS_AF",
"gnomAD_exomes_controls_EAS_nhomalt",
"gnomAD_exomes_controls_FIN_AC",
"gnomAD_exomes_controls_FIN_AN",
"gnomAD_exomes_controls_FIN_AF",
"gnomAD_exomes_controls_FIN_nhomalt",
"gnomAD_exomes_controls_NFE_AC",
"gnomAD_exomes_controls_NFE_AN",
"gnomAD_exomes_controls_NFE_AF",
"gnomAD_exomes_controls_NFE_nhomalt",
"gnomAD_exomes_controls_SAS_AC",
"gnomAD_exomes_controls_SAS_AN",
"gnomAD_exomes_controls_SAS_AF",
"gnomAD_exomes_controls_SAS_nhomalt",
"gnomAD_exomes_controls_POPMAX_AC",
"gnomAD_exomes_controls_POPMAX_AN",
"gnomAD_exomes_controls_POPMAX_AF",
"gnomAD_exomes_controls_POPMAX_nhomalt",
"gnomAD_genomes_flag",
"gnomAD_genomes_AC",
"gnomAD_genomes_AN",
"gnomAD_genomes_AF",
"gnomAD_genomes_nhomalt",
"gnomAD_genomes_AFR_AC",
"gnomAD_genomes_AFR_AN",
"gnomAD_genomes_AFR_AF",
"gnomAD_genomes_AFR_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_NFE_AC",
"gnomAD_genomes_NFE_AN",
"gnomAD_genomes_NFE_AF",
"gnomAD_genomes_NFE_nhomalt",
"gnomAD_genomes_AMI_AC",
"gnomAD_genomes_AMI_AN",
"gnomAD_genomes_AMI_AF",
"gnomAD_genomes_AMI_nhomalt",
"gnomAD_genomes_SAS_AC",
"gnomAD_genomes_SAS_AN",
"gnomAD_genomes_SAS_AF",
"gnomAD_genomes_SAS_nhomalt",
"gnomAD_genomes_POPMAX_AC",
"gnomAD_genomes_POPMAX_AN",
"gnomAD_genomes_POPMAX_AF",
"gnomAD_genomes_POPMAX_nhomalt",
"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_gene",
"GTEx_V8_tissue",
"Geuvadis_eQTL_target_gene"
],
},
]
},
# CADD
# https://github.com/ensembl-variation/VEP_plugins/blob/master/CADD.pm
# Requires tabix-indexed data file as first param
# No other parameters so no form required
# data file currently only available for GRCh37
{
"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.",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/102/CADD.pm",
"requires_data" => 1,
"species" => [
"homo_sapiens"
],
"params" => [
#"/path/to/whole_genome_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/102/FATHMM.pm"
},
# FATHMM-MKL
# https://github.com/ensembl-variation/VEP_plugins/blob/master/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/102/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/master/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/102/Carol.pm",
"requires_install" => 1,
"species" => [
"homo_sapiens"
],
},
# Condel
# https://github.com/ensembl-variation/VEP_plugins/blob/master/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/102/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/102/LoFtool.pm",
"requires_data" => 1,
"species" => [
"homo_sapiens"
],
"params" => [
# "/path/to/LoFtool_scores.txt"
]
},
# ExACpLI
# Requires ExACpLI_values.txt file as first param (available in VEP_plugins GitHub repo)
{
"key" => "ExACpLI",
"helptip" => "Provides a per-gene probability of being loss-of-function intolerant (pLI) from ExAC data",
"available" => 0,
"enabled" => 0,
"section" => "Pathogenicity predictions",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/102/ExACpLI.pm",
"requires_data" => 1,
"species" => [
"homo_sapiens"
],
"params" => [
# "/path/to/ExACpLI_values.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/102/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/102/MTR.pm",
"requires_data" => 1,
"species" => [
"homo_sapiens"
],
"params" => [
# "/path/to/mtrflatfile_1.0.txt.gz"
]
},
# 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/102/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/102/PON_P2.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/102/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/102/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/102/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/102/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/102/SpliceAI.pm",
},
## CONSERVATION
###############
# Blosum62
{
"key" => "Blosum62",
"label" => "BLOSUM62",
"helptip" => "BLOSUM62 amino acid conservation score",
"available" => 0,
"enabled" => 0,
"section" => "Conservation",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/102/Blosum62.pm",
},
# Conservation
# Use the following query to get valid species sets:
#
# SELECT group_concat(concat("_stt_", gd.name) SEPARATOR ' '), REPLACE(mlss.name, "Gerp Conservation Scores ", ""), sst.value
# FROM method_link ml,
# method_link_species_set mlss,
# genome_db gd, species_set ss, species_set_tag sst
# WHERE mlss.method_link_id = ml.method_link_id AND
# mlss.species_set_id = ss.species_set_id AND
# ss.genome_db_id = gd.genome_db_id AND
# ss.species_set_id = sst.species_set_id AND
# (ml.class = "ConservationScore.conservation_score")
# GROUP BY mlss.species_set_id
{
"key" => "Conservation",
"helptip" => "Retrieves a conservation score from the Ensembl Compara databases for variant positions",
"available" => 0,
"enabled" => 0,
"section" => "Conservation",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/102/Conservation.pm",
"params" => [
"@*"
],
"form" => [
{
"name" => "method_link_type",
"label" => "Method",
"type" => "dropdown",
"values" => [
{ "value" => "GERP_CONSERVATION_SCORE", "caption" => "GERP"}
]
},
{
"name" => "species_set",
"label" => "Species set",
"type" => "dropdown",
"values" => [
{ "value" => "mammals", "caption" => "39 eutherian mammals" }, #"class" => "_stt_macaca_mulatta _stt_echinops_telfairi _stt_tupaia_belangeri _stt_erinaceus_europaeus _stt_sorex_araneus _stt_microcebus_murinus _stt_pongo_abelii _stt_equus_caballus _stt_ochotona_princeps _stt_cavia_porcellus _stt_choloepus_hoffmanni _stt_procavia_capensis _stt_tursiops_truncatus _stt_tarsius_syrichta _stt_dipodomys_ordii _stt_vicugna_pacos _stt_pteropus_vampyrus _stt_loxodonta_africana _stt_oryctolagus_cuniculus _stt_ailuropoda_melanoleuca _stt_nomascus_leucogenys _stt_callithrix_jacchus _stt_myotis_lucifugus _stt_bos_taurus _stt_gorilla_gorilla _stt_otolemur_garnettii _stt_pan_troglodytes _stt_ictidomys_tridecemlineatus _stt_sus_scrofa _stt_mus_musculus _stt_canis_familiaris _stt_mustela_putorius_furo _stt_felis_catus _stt_ovis_aries _stt_dasypus_novemcinctus _stt_homo_sapiens _stt_papio_anubis _stt_chlorocebus_sabaeus _stt_rattus_norvegicus" },
{ "value" => "amniotes", "caption" => "23 amniota vertebrates" }, #"class" => "_stt_macaca_mulatta _stt_ornithorhynchus_anatinus _stt_monodelphis_domestica _stt_pongo_abelii _stt_equus_caballus _stt_taeniopygia_guttata _stt_oryctolagus_cuniculus _stt_anolis_carolinensis _stt_meleagris_gallopavo _stt_callithrix_jacchus _stt_bos_taurus _stt_gorilla_gorilla _stt_pan_troglodytes _stt_sus_scrofa _stt_mus_musculus _stt_canis_familiaris _stt_felis_catus _stt_gallus_gallus _stt_ovis_aries _stt_homo_sapiens _stt_papio_anubis _stt_chlorocebus_sabaeus _stt_rattus_norvegicus" },
{ "value" => "sauropsids", "caption" => "7 sauropsids" }, #"class" => "_stt_taeniopygia_guttata _stt_anolis_carolinensis _stt_meleagris_gallopavo _stt_pelodiscus_sinensis _stt_gallus_gallus _stt_anas_platyrhynchos _stt_ficedula_albicollis" },
{ "value" => "fish", "caption" => "11 fish" }, #"class" => "_stt_takifugu_rubripes _stt_gasterosteus_aculeatus _stt_oryzias_latipes _stt_tetraodon_nigroviridis _stt_gadus_morhua _stt_oreochromis_niloticus _stt_xiphophorus_maculatus _stt_astyanax_mexicanus _stt_lepisosteus_oculatus _stt_poecilia_formosa _stt_danio_rerio" },
]
},
]
},
# AncestralAllele
# Requires processed FASTA file from ftp://ftp.ensembl.org/pub/current_fasta/ancestral_alleles/
{
"key" => "AncestralAllele",
"label" => "Ancestral allele",
"helptip" => "Retrieves the ancestral allele for variants inferred from the Ensembl Compara Enredo-Pecan-Ortheus (EPO) pipeline",
"available" => 0,
"enabled" => 0,
"section" => "Conservation",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/102/AncestralAllele.pm",
"requires_data" => 1,
"species" => [
"homo_sapiens"
],
"params" => [
# "/path/to/homo_sapiens_ancestor_GRCh38_e93.fa.gz"
]
},
## FREQUENCY DATA
#################
# ExAC
{
"key" => "ExAC",
"label" => "ExAC frequencies",
"helptip" => "Reports allele frequencies from the Exome Aggregation Consortium",
"available" => 0,
"enabled" => 0,
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/102/ExAC.pm",
"section" => "Frequency data",
"requires_data" => 1,
"species" => [
"homo_sapiens"
],
"params" => [
# "/path/to/ExAC.r0.3.sites.vep.vcf.gz"
]
},
# gnomADc
{
"key" => "gnomADc",
"label" => "gnomADc",
"available" => 0,
"enabled" => 0,
"section" => "Frequency data",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/102/gnomADc.pm"
},
## PHENOTYPES DATA
##################
# Phenotypes
{
"key" => "Phenotypes",
"label" => "Phenotypes",
"helptip" => "Retrieves overlapping phenotype annotations",
"section" => "Phenotype data",
"requires_data" => 1,
"available" => 0,
"enabled" => 0,
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/102/Phenotypes.pm",
"params" => [
#"/path/to/Phenotypes_data_files/phenotypes_dir_with_dumps_for_all_species.gvf.gz"
]
},
# GO
{
"key" => "GO",
"label" => "Gene Ontology",
"helptip" => "Retrieves Gene Ontology terms associated with transcripts/translations via the Ensembl API",
"available" => 0,
"enabled" => 0,
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/102/GO.pm",
"section" => "Phenotype data",
},
# G2P
{
"key" => "G2P",
"label" => "G2P",
"helptip" => "Assesses variants using G2P allelic requirements for potential phenotype involvement.",
"available" => 0,
"enabled" => 0,
"requires_data" => 1,
"section" => "Phenotype data",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/102/G2P.pm",
},
# PostGAP
{
"key" => "PostGAP",
"label" => "PostGAP",
"available" => 0,
"enabled" => 0,
"section" => "Phenotype data",
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/102/PostGAP.pm"
},
# satMutMPRA
{
"key" => "satMutMPRA",
"helptip" => "Reports saturation mutagenesis MPRA measures of variant effects on gene RNA expression for 21 enhancers/promoters",
"section" => "Phenotype data",
"available" => 0,
"enabled" => 0,
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/102/satMutMPRA.pm",
},
# DisGeNET
{
"key" => "DisGeNET",
"helptip" => "Variant-Disease-PMID associations from the DisGeNET database (https://www.disgenet.org/)",
"section" => "Phenotype data",
"available" => 0,
"enabled" => 0,
"species" => [
"homo_sapiens"
],
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/102/DisGeNET.pm",
},
## VARIANT DATA
###############
# LD
{
"key" => "LD",
"label" => "Linkage disequilibrium",
"helptip" => "Finds variants in linkage disequilibrium with any overlapping existing variants from the Ensembl variation databases",
"available" => 0,
"enabled" => 0,
"plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/102/LD.pm",
"section" => "Variant data",
"params" => [
"@*"
],
"form" => [
{
"name" => "population",
"label" => "Population",
"type" => "dropdown",
"values" => [
{ "value" => "1000GENOMES:phase_3:ACB", "caption" => "African Caribbean in Barbados" },
{ "value" => "1000GENOMES:phase_3:ASW", "caption" => "African Ancestry in Southwest US" },
{ "value" => "1000GENOMES:phase_3:BEB", "caption" => "Bengali in Bangladesh" },
{ "value" => "1000GENOMES:phase_3:CDX", "caption" => "Chinese Dai in Xishuangbanna, China" },
{ "value" => "1000GENOMES:phase_3:CEU", "caption" => "Utah residents with Northern and Western European ancestry" },
{ "value" => "1000GENOMES:phase_3:CHB", "caption" => "Han Chinese in Bejing, China" },
{ "value" => "1000GENOMES:phase_3:CHS", "caption" => "Southern Han Chinese, China" },
{ "value" => "1000GENOMES:phase_3:CLM", "caption" => "Colombian in Medellin, Colombia" },
{ "value" => "1000GENOMES:phase_3:ESN", "caption" => "Esan in Nigeria" },
{ "value" => "1000GENOMES:phase_3:FIN", "caption" => "Finnish in Finland" },
{ "value" => "1000GENOMES:phase_3:GBR", "caption" => "British in England and Scotland" },
{ "value" => "1000GENOMES:phase_3:GIH", "caption" => "Gujarati Indian in Houston, TX" },
{ "value" => "1000GENOMES:phase_3:IBS", "caption" => "Iberian populations in Spain" },
{ "value" => "1000GENOMES:phase_3:ITU", "caption" => "Indian Telugu in the UK" },
{ "value" => "1000GENOMES:phase_3:JPT", "caption" => "Japanese in Tokyo, Japan" },
{ "value" => "1000GENOMES:phase_3:KHV", "caption" => "Kinh in Ho Chi Minh City, Vietnam" },
{ "value" => "1000GENOMES:phase_3:LWK", "caption" => "Luhya in Webuye, Kenya" },
{ "value" => "1000GENOMES:phase_3:MAG", "caption" => "Mandinka in The Gambia" },
{ "value" => "1000GENOMES:phase_3:MSL", "caption" => "Mende in Sierra Leone" },
{ "value" => "1000GENOMES:phase_3:MXL", "caption" => "Mexican Ancestry in Los Angeles, California" },
{ "value" => "1000GENOMES:phase_3:PEL", "caption" => "Peruvian in Lima, Peru" },
{ "value" => "1000GENOMES:phase_3:PJL", "caption" => "Punjabi in Lahore, Pakistan" },
{ "value" => "1000GENOMES:phase_3:PUR", "caption" => "Puerto Rican in Puerto Rico" },
{ "value" => "1000GENOMES:phase_3:STU", "caption" => "Sri Lankan Tamil in the UK" },
{ "value" => "1000GENOMES:phase_3:TSI", "caption" => "Toscani in Italy" },
{ "value" => "1000GENOMES:phase_3:YRI", "caption" => "Yoruba in Ibadan, Nigeria" },
],
"value" => "1000GENOMES:phase_3:CEU",
},
{
"name" => "threshold",
"label" => "r2 cutoff",
"type" => "string",
"value" => 0.8,
},
]