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
    {
      "key" => "dbNSFP",
      "label" => "dbNSFP",
      "available" => 1,
      "enabled" => 0,
      "section" => "Pathogenicity predictions",
      "helptip" => "dbNSFP provides pathogenicity predictions for missense variants from various algorithms",
      "plugin_url" => "https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/dbNSFP.pm",
      "requires_data" => 1,
      "requires_install" => 1,
      "params"  => [
        #"/path/to/dbNSFP3.0b1a.txt.gz",
        "@*"
      ],
      "species" => [
        "homo_sapiens"
      ],
      "form" => [
        {
          "name" => "dbNSFP_fields",
          "label" => "Fields to include",
          "helptip" => "A comma-separated list of fields to fetch from dbNSFP; start typing to see available fields",
          "value" => "",
          "type" => "string",
          "class" => "autocomplete-multi",
          "values" => [
            "chr",
            "pos(1-based)",
            "ref",
            "alt",
            "aaref",
            "aaalt",
            "rs_dbSNP142",
            "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",
            "Uniprot_id_MutationAssessor",
            "Uniprot_variant_MutationAssessor",
            "MutationAssessor_score",
            "MutationAssessor_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",
            "CADD_raw",
            "CADD_raw_rankscore",
            "CADD_phred",
            "MetaSVM_score",
            "MetaSVM_rankscore",
            "MetaSVM_pred",
            "MetaLR_score",
            "MetaLR_rankscore",
            "MetaLR_pred",
            "Reliability_index",
            "GERP++_NR",
            "GERP++_RS",
            "GERP++_RS_rankscore",
            "phyloP7way_vertebrate",
            "phyloP7way_vertebrate_rankscore",
            "phastCons7way_vertebrate",
            "phastCons7way_vertebrate_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",
            "clinvar_rs",
            "clinvar_clnsig",
            "clinvar_trait",
            "Interpro_domain"
          ],
        },
      ]
    },

    # 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-variation/VEP_plugins/master/CADD.pm",
      "requires_data" => 1,
      "species" => [
        "homo_sapiens"
      ],
      "params" => [
        #"/path/to/whole_genome_SNVs.tsv.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-variation/VEP_plugins/master/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" => 1,
      "enabled" => 0,
      "section" => "Pathogenicity predictions",
      "plugin_url" => "https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/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",
        },
      ],
    },

    # LoFtool
    # Requires LoFtool_scores.txt file as first param (available in VEP_plugins GitHub repo)
    {
      "key" => "LoFtool",
      "helptip" => "Provides a rank of genic intolerance and consequent susceptibility to disease based on the ratio of Loss-of-function (LoF) to synonymous mutations",
      "available" => 1,
      "enabled" => 0,
      "section" => "Pathogenicity predictions",
      "plugin_url" => "https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/LoFtool.pm",
      "requires_data" => 1,
      "species" => [
        "homo_sapiens"
      ],
      "params" => [
        # "/path/to/LoFtool_scores.txt"
      ]
    },


    ## CONSERVATION
    ###############

    # Blosum62
    {
      "key" => "Blosum62",
      "label" => "BLOSUM62",
      "helptip" => "BLOSUM62 amino acid conservation score",
      "available" => 1,
      "enabled" => 0,
      "section" => "Conservation",
      "plugin_url" => "https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/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" => 1,
      "enabled" => 0,
      "section" => "Conservation",
      "plugin_url" => "https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/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" },
          ]
        },
      ]
    },


    ## VARIANT NOTATION
    ###################

    # CSN
    {
      "key" => "CSN",
      "helptip" => "Reports Clinical Sequencing Nomenclature (CSN) for variants",
      "available" => 1,
      "enabled" => 0,
      "section" => "Variant notation",
      "plugin_url" => "https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/CSN.pm",
    },

    # HGVSshift
    {
      "key" => "HGVSshift",
      "label" => "Unshifted HGVS",
      "helptip" => "By default VEP 3' shifts HGVS notations in repetetive sequence; use this plugin to additionally report unshifted notations",
      "available" => 1,
      "enabled" => 0,
      "section" => "Variant notation",
      "plugin_url" => "https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/HGVSshift.pm",
    },


    ## OTHER
    ########

    # ExAC
    {
      "key" => "ExAC",
      "helptip" => "Reports allele frequencies from the Exome Aggregation Consortium",
      "available" => 1,
      "enabled" => 0,
      "plugin_url" => "https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/ExAC.pm",
      "requires_data" => 1,
      "species" => [
        "homo_sapiens"
      ],
      "params" => [
        # "/path/to/ExAC.r0.3.sites.vep.vcf.gz"
      ]
    },

    # miRNA
    {
      "key" => "miRNA",
      "label" => "miRNA structure",
      "helptip" => "Determines where in the secondary structure of a miRNA a variant falls",
      "available" => 1,
      "enabled" => 0,
      "plugin_url" => "https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/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" => 1,
      "enabled" => 0,
      "helptip" => "Change the distance to transcript (in bp) for which VEP assigns upstream and downstream consequences",
      "plugin_url" => "https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/UpDownDistance.pm",
      "params" => [
        "@*"
      ],
      "form" => [
        {
          "name" => "distance",
          "label" => "Distance (bp)",
          "type" => "string",
          "value" => 5000
        }
      ]
    },
  ]
};