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view dir_plugins/plugin_config.txt @ 0:e545d0a25ffe draft
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| author | dvanzessen |
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| date | Mon, 15 Jul 2019 05:17:17 -0400 |
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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/94/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/94/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/94/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/94/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/94/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/94/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/94/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/94/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/94/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/94/REVEL.pm", "requires_data" => 1, "species" => [ "homo_sapiens" ], "params" => [ # "/path/to/revel_all_chromosomes.tsv.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/94/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/94/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/94/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/94/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/94/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/94/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/94/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/94/ExAC.pm", "section" => "Frequency data", "requires_data" => 1, "species" => [ "homo_sapiens" ], "params" => [ # "/path/to/ExAC.r0.3.sites.vep.vcf.gz" ] }, ## OTHER ######## # CSN { "key" => "CSN", "helptip" => "Reports Clinical Sequencing Nomenclature (CSN) for variants", "available" => 0, "enabled" => 0, "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/CSN.pm", }, # 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/94/miRNA.pm", }, # 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/94/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/94/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/94/SameCodon.pm", "section" => "Variant data", }, # LOVD { "key" => "LOVD", "label" => "LOVD", "helptip" => "Retrieves LOVD variation data", "available" => 0, "enabled" => 0, "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/LOVD.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/94/GO.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/94/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/94/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/94/TSSDistance.pm", }, # Phenotypes { "key" => "Phenotypes", "label" => "Phenotypes", "helptip" => "Retrieves overlapping phenotype annotations", "available" => 0, "enabled" => 0, "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/Phenotypes.pm", }, # Draw { "key" => "Draw", "label" => "Draw", "helptip" => "Creates images of the transcript model showing variant location", "available" => 0, "enabled" => 0, "requires_install" => 1, "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/Draw.pm", }, # G2P { "key" => "G2P", "label" => "G2P", "helptip" => "Assesses variants using G2P allelic requirements for potential phenotype involvement.", "available" => 0, "enabled" => 0, "requires_data" => 1, "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/G2P.pm", }, # LocalID { "key" => "LocalID", "label" => "LocalID", "helptip" => "Allows you to use variant IDs as VEP input without making a database connection.", "available" => 0, "enabled" => 0, "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/LocalID.pm", }, ] };