plugin_config.txt

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/91/dbNSFP.pm",
      "requires_data" => 1,
      "requires_install" => 1,
      "params"  => [
        #"/path/to/dbNSFP3.5a.txt.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/0B60wROKy6OqcNGJ2STJlMTJONk0/view">dbNSFP README</a>',
          # "class" => "jquery-multiselect",
          "values" => [
            # "chr",
            # "pos(1-based)",
            # "ref",
            # "alt",
            # "aaref",
            # "aaalt",
            # "rs_dbSNP150",
            # "hg19_chr",
            # "hg19_pos(1-based)",
            # "hg18_chr",
            # "hg18_pos(1-based)",
            # "genename",
            # "cds_strand",
            # "refcodon",
            # "codonpos",
            "codon_degeneracy",
            "Ancestral_allele",
            "AltaiNeandertal",
            "Denisova",
            # "Ensembl_geneid",
            # "Ensembl_transcriptid",
            # "Ensembl_proteinid",
            # "aapos",
            # "SIFT_score",
            # "SIFT_converted_rankscore",
            # "SIFT_pred",
            # "Uniprot_acc_Polyphen2",
            # "Uniprot_id_Polyphen2",
            # "Uniprot_aapos_Polyphen2",
            # "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_UniprotID",
            "MutationAssessor_variant",
            "MutationAssessor_score",
            "MutationAssessor_score_rankscore",
            "MutationAssessor_pred",
            "FATHMM_score",
            "FATHMM_converted_rankscore",
            "FATHMM_pred",
            "PROVEAN_score",
            "PROVEAN_converted_rankscore",
            "PROVEAN_pred",
            "Transcript_id_VEST3",
            "Transcript_var_VEST3",
            "VEST3_score",
            "VEST3_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",
            "CADD_raw",
            "CADD_raw_rankscore",
            "CADD_phred",
            "DANN_score",
            "DANN_rankscore",
            "fathmm-MKL_coding_score",
            "fathmm-MKL_coding_rankscore",
            "fathmm-MKL_coding_pred",
            "fathmm-MKL_coding_group",
            "Eigen_coding_or_noncoding",
            "Eigen-raw",
            "Eigen-phred",
            "Eigen-PC-raw",
            "Eigen-PC-phred",
            "Eigen-PC-raw_rankscore",
            "GenoCanyon_score",
            "GenoCanyon_score_rankscore",
            "integrated_fitCons_score",
            "integrated_fitCons_score_rankscore",
            "integrated_confidence_value",
            "GM12878_fitCons_score",
            "GM12878_fitCons_score_rankscore",
            "GM12878_confidence_value",
            "H1-hESC_fitCons_score",
            "H1-hESC_fitCons_score_rankscore",
            "H1-hESC_confidence_value",
            "HUVEC_fitCons_score",
            "HUVEC_fitCons_score_rankscore",
            "HUVEC_confidence_value",
            "GERP++_NR",
            "GERP++_RS",
            "GERP++_RS_rankscore",
            "phyloP100way_vertebrate",
            "phyloP100way_vertebrate_rankscore",
            "phyloP20way_mammalian",
            "phyloP20way_mammalian_rankscore",
            "phastCons100way_vertebrate",
            "phastCons100way_vertebrate_rankscore",
            "phastCons20way_mammalian",
            "phastCons20way_mammalian_rankscore",
            "SiPhy_29way_pi",
            "SiPhy_29way_logOdds",
            "SiPhy_29way_logOdds_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",
            "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_AC",
            "gnomAD_exomes_AN",
            "gnomAD_exomes_AF",
            "gnomAD_exomes_AFR_AC",
            "gnomAD_exomes_AFR_AN",
            "gnomAD_exomes_AFR_AF",
            "gnomAD_exomes_AMR_AC",
            "gnomAD_exomes_AMR_AN",
            "gnomAD_exomes_AMR_AF",
            "gnomAD_exomes_ASJ_AC",
            "gnomAD_exomes_ASJ_AN",
            "gnomAD_exomes_ASJ_AF",
            "gnomAD_exomes_EAS_AC",
            "gnomAD_exomes_EAS_AN",
            "gnomAD_exomes_EAS_AF",
            "gnomAD_exomes_FIN_AC",
            "gnomAD_exomes_FIN_AN",
            "gnomAD_exomes_FIN_AF",
            "gnomAD_exomes_NFE_AC",
            "gnomAD_exomes_NFE_AN",
            "gnomAD_exomes_NFE_AF",
            "gnomAD_exomes_SAS_AC",
            "gnomAD_exomes_SAS_AN",
            "gnomAD_exomes_SAS_AF",
            "gnomAD_exomes_OTH_AC",
            "gnomAD_exomes_OTH_AN",
            "gnomAD_exomes_OTH_AF",
            "gnomAD_genomes_AC",
            "gnomAD_genomes_AN",
            "gnomAD_genomes_AF",
            "gnomAD_genomes_AFR_AC",
            "gnomAD_genomes_AFR_AN",
            "gnomAD_genomes_AFR_AF",
            "gnomAD_genomes_AMR_AC",
            "gnomAD_genomes_AMR_AN",
            "gnomAD_genomes_AMR_AF",
            "gnomAD_genomes_ASJ_AC",
            "gnomAD_genomes_ASJ_AN",
            "gnomAD_genomes_ASJ_AF",
            "gnomAD_genomes_EAS_AC",
            "gnomAD_genomes_EAS_AN",
            "gnomAD_genomes_EAS_AF",
            "gnomAD_genomes_FIN_AC",
            "gnomAD_genomes_FIN_AN",
            "gnomAD_genomes_FIN_AF",
            "gnomAD_genomes_NFE_AC",
            "gnomAD_genomes_NFE_AN",
            "gnomAD_genomes_NFE_AF",
            "gnomAD_genomes_OTH_AC",
            "gnomAD_genomes_OTH_AN",
            "gnomAD_genomes_OTH_AF",
            "clinvar_rs",
            "clinvar_clnsig",
            "clinvar_trait",
            "clinvar_golden_stars",
            "Interpro_domain",
            "GTEx_V6p_gene",
            "GTEx_V6p_tissue"
          ],
        },
      ]
    },
    
    # 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/91/CADD.pm",
      "requires_data" => 1,
      "species" => [
        "homo_sapiens"
      ],
      "params" => [
        #"/path/to/whole_genome_SNVs.tsv.gz"
      ]
    },
    
    # 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/91/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/91/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/91/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",
        },
      ],
    },

    # PolyPhen_SIFT
    {
      "key" => "PolyPhen_SIFT",
      "helptip" => "Retrieves PolyPhen and SIFT predictions from a locally constructed sqlite database",
      "available" => 0,
      "enabled" => 0,
      "section" => "Pathogenicity predictions",
      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/91/PolyPhen_SIFT.pm",
      "requires_install" => 1,
      "species" => [
        "homo_sapiens"
      ],
      "params" => [
        "@*"
      ],
    },

    # 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/91/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/91/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/91/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/91/MTR.pm",
      "requires_data" => 1,
      "species" => [
        "homo_sapiens"
      ],
      "params" => [
        # "/path/to/mtrflatfile_1.0.txt.gz"
      ]
    },


    
    ## 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/91/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/91/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/91/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/91/SpliceRegion.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/91/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/91/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/91/AncestralAllele.pm",
      "requires_data" => 1,
      "species" => [
        "homo_sapiens"
      ],
      "params" => [
        # "/path/to/homo_sapiens_ancestor_GRCh38_e91.fa.gz"
      ]
    },


    ## IDENTIFIERS
    ##############

    # CSN
    {
      "key" => "CSN",
      "helptip" => "Reports Clinical Sequencing Nomenclature (CSN) for variants",
      "available" => 0,
      "enabled" => 0,
      "section" => "Identifiers",
      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/91/CSN.pm",
    },
    

    ## 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/91/ExAC.pm",
      "section" => "Frequency data",
      "requires_data" => 1,
      "species" => [
        "homo_sapiens"
      ],
      "params" => [
        # "/path/to/ExAC.r0.3.sites.vep.vcf.gz"
      ]
    },


    ## OTHER
    ########

    # miRNA
    {
      "key" => "miRNA",
      "label" => "miRNA structure",
      "helptip" => "Determines where in the secondary structure of a miRNA a variant falls",
      "available" => 0,
      "enabled" => 0,
      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/91/miRNA.pm",
    },
    

    # UpDownDistance
    # https://github.com/ensembl-variation/VEP_plugins/blob/master/UpDownDistance.pm
    # Sets the upstream/downstream search distance either side of transcripts
    {
      "key" => "UpDownDistance",
      "label" => "Upstream/Downstream distance",
      "available" => 0,
      "enabled" => 0,
      "helptip" => "Change the distance to transcript (default is 5000bp) for which VEP assigns upstream and downstream consequences",
      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/91/UpDownDistance.pm",
      "params" => [
        "@*"
      ],
      "form" => [
        {
          "name" => "distance",
          "label" => "Distance (bp)",
          "type" => "string",
          "value" => 5000
        }
      ]
    },

    # NearestGene
    {
      "key" => "NearestGene",
      "label" => "Nearest gene",
      "helptip" => "Finds the nearest gene to non-genic variants",
      "available" => 0,
      "enabled" => 0,
      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/91/NearestGene.pm",
    },

    # 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/91/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,
        },
      ]
    },

    # SameCodon
    {
      "key" => "SameCodon",
      "label" => "Variants in same codon",
      "helptip" => "Reports existing variants that fall in the same codon",
      "available" => 0,
      "enabled" => 0,
      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/91/SameCodon.pm",
      "section" => "Variant data",
    },

    # 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/91/GO.pm",
      "section" => "Gene data",
    },

    # GXA
    {
      "key" => "GXA",
      "label" => "Gene Expression Atlas",
      "helptip" => "Reports data from the Gene Expression Atlas",
      "available" => 0,
      "enabled" => 0,
      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/91/GXA.pm",
      "section" => "Gene data",
    },

    # Downstream
    {
      "key" => "Downstream",
      "label" => "Downstream",
      "helptip" => "Predicts the downstream effects of a frameshift variant on the protein sequence of a transcript",
      "available" => 0,
      "enabled" => 0,
      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/91/Downstream.pm",
    },

    # ProteinSeqs
    {
      "key" => "ProteinSeqs",
      "label" => "Protein sequences",
      "helptip" => "Prints out the reference and mutated protein sequences of any proteins found with non-synonymous mutations",
      "available" => 0,
      "enabled" => 0,
      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/91/ProteinSeqs.pm",
    },

    # TSSDistance
    {
      "key" => "TSSDistance",
      "label" => "TSS distance",
      "helptip" => "Calculates the distance from the transcription start site for upstream variants   ",
      "available" => 0,
      "enabled" => 0,
      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/91/TSSDistance.pm",
    },
  ]
};