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1 my $VEP_PLUGIN_CONFIG = {
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2 "plugins" => [
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3
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4 ## PATHOGENICITY PREDICTIONS
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5 ############################
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6
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7 # dbNSFP
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8 # https://github.com/ensembl-variation/VEP_plugins/blob/master/dbNSFP.pm
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9 # Requires tabix-indexed data file as first param
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10 # Field names are listed below and rendered as a multi-selectable autocomplete text field
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11 # Human, GRCh38 only (3.x), for GRCh37 use 2.9.x
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12 {
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13 "key" => "dbNSFP",
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14 "label" => "dbNSFP",
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15 "available" => 0,
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16 "enabled" => 0,
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17 "section" => "Pathogenicity predictions",
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18 "helptip" => "dbNSFP provides pathogenicity predictions for missense variants from various algorithms",
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19 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/dbNSFP.pm",
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20 "requires_data" => 1,
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21 "requires_install" => 1,
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22 "params" => [
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23 #"/path/to/dbNSFP3.5a.txt.gz",
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24 "@*"
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25 ],
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26 "species" => [
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27 "homo_sapiens"
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28 ],
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29 "form" => [
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30 {
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31 "name" => "dbNSFP_fields",
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32 "label" => "Fields to include",
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33 "helptip" => "Fields to fetch from dbNSFP; hold down the Ctrl (Windows) / Command (Mac) button to select multiple options",
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34 "value" => "",
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35 'type' => 'dropdown',
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36 'multiple' => 1,
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37 'style' => 'height:150px',
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38 'required' => 1,
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39 'notes' => 'Field descriptions in <a rel="external" href="https://drive.google.com/file/d/0B60wROKy6OqcNGJ2STJlMTJONk0/view">dbNSFP README</a>',
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40 # "class" => "jquery-multiselect",
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41 "values" => [
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42 # "chr",
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43 # "pos(1-based)",
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44 # "ref",
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45 # "alt",
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46 # "aaref",
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47 # "aaalt",
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48 # "rs_dbSNP150",
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49 # "hg19_chr",
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50 # "hg19_pos(1-based)",
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51 # "hg18_chr",
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52 # "hg18_pos(1-based)",
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53 # "genename",
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54 # "cds_strand",
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55 # "refcodon",
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56 # "codonpos",
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57 "codon_degeneracy",
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58 "Ancestral_allele",
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59 "AltaiNeandertal",
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60 "Denisova",
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61 # "Ensembl_geneid",
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62 # "Ensembl_transcriptid",
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63 # "Ensembl_proteinid",
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64 # "aapos",
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65 # "SIFT_score",
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66 # "SIFT_converted_rankscore",
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67 # "SIFT_pred",
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68 # "Uniprot_acc_Polyphen2",
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69 # "Uniprot_id_Polyphen2",
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70 # "Uniprot_aapos_Polyphen2",
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71 # "Polyphen2_HDIV_score",
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72 # "Polyphen2_HDIV_rankscore",
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73 # "Polyphen2_HDIV_pred",
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74 # "Polyphen2_HVAR_score",
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75 # "Polyphen2_HVAR_rankscore",
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76 # "Polyphen2_HVAR_pred",
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77 "LRT_score",
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78 "LRT_converted_rankscore",
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79 "LRT_pred",
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80 "LRT_Omega",
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81 "MutationTaster_score",
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82 "MutationTaster_converted_rankscore",
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83 "MutationTaster_pred",
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84 "MutationTaster_model",
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85 "MutationTaster_AAE",
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86 "MutationAssessor_UniprotID",
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87 "MutationAssessor_variant",
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88 "MutationAssessor_score",
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89 "MutationAssessor_score_rankscore",
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90 "MutationAssessor_pred",
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91 "FATHMM_score",
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92 "FATHMM_converted_rankscore",
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93 "FATHMM_pred",
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94 "PROVEAN_score",
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95 "PROVEAN_converted_rankscore",
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96 "PROVEAN_pred",
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97 "Transcript_id_VEST3",
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98 "Transcript_var_VEST3",
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99 "VEST3_score",
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100 "VEST3_rankscore",
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101 "MetaSVM_score",
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102 "MetaSVM_rankscore",
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103 "MetaSVM_pred",
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104 "MetaLR_score",
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105 "MetaLR_rankscore",
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106 "MetaLR_pred",
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107 "Reliability_index",
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108 "M-CAP_score",
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109 "M-CAP_rankscore",
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110 "M-CAP_pred",
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111 "REVEL_score",
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112 "REVEL_rankscore",
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113 "MutPred_score",
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114 "MutPred_rankscore",
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115 "MutPred_protID",
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116 "MutPred_AAchange",
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117 "MutPred_Top5features",
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118 "CADD_raw",
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119 "CADD_raw_rankscore",
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120 "CADD_phred",
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121 "DANN_score",
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122 "DANN_rankscore",
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123 "fathmm-MKL_coding_score",
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124 "fathmm-MKL_coding_rankscore",
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125 "fathmm-MKL_coding_pred",
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126 "fathmm-MKL_coding_group",
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127 "Eigen_coding_or_noncoding",
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128 "Eigen-raw",
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129 "Eigen-phred",
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130 "Eigen-PC-raw",
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131 "Eigen-PC-phred",
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132 "Eigen-PC-raw_rankscore",
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133 "GenoCanyon_score",
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134 "GenoCanyon_score_rankscore",
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135 "integrated_fitCons_score",
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136 "integrated_fitCons_score_rankscore",
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137 "integrated_confidence_value",
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138 "GM12878_fitCons_score",
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139 "GM12878_fitCons_score_rankscore",
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140 "GM12878_confidence_value",
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141 "H1-hESC_fitCons_score",
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142 "H1-hESC_fitCons_score_rankscore",
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143 "H1-hESC_confidence_value",
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144 "HUVEC_fitCons_score",
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145 "HUVEC_fitCons_score_rankscore",
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146 "HUVEC_confidence_value",
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147 "GERP++_NR",
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148 "GERP++_RS",
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149 "GERP++_RS_rankscore",
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150 "phyloP100way_vertebrate",
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151 "phyloP100way_vertebrate_rankscore",
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152 "phyloP20way_mammalian",
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153 "phyloP20way_mammalian_rankscore",
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154 "phastCons100way_vertebrate",
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155 "phastCons100way_vertebrate_rankscore",
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156 "phastCons20way_mammalian",
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157 "phastCons20way_mammalian_rankscore",
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158 "SiPhy_29way_pi",
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159 "SiPhy_29way_logOdds",
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160 "SiPhy_29way_logOdds_rankscore",
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161 "1000Gp3_AC",
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162 "1000Gp3_AF",
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163 "1000Gp3_AFR_AC",
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164 "1000Gp3_AFR_AF",
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165 "1000Gp3_EUR_AC",
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166 "1000Gp3_EUR_AF",
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167 "1000Gp3_AMR_AC",
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168 "1000Gp3_AMR_AF",
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169 "1000Gp3_EAS_AC",
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170 "1000Gp3_EAS_AF",
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171 "1000Gp3_SAS_AC",
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172 "1000Gp3_SAS_AF",
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173 "TWINSUK_AC",
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174 "TWINSUK_AF",
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175 "ALSPAC_AC",
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176 "ALSPAC_AF",
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177 "ESP6500_AA_AC",
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178 "ESP6500_AA_AF",
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179 "ESP6500_EA_AC",
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180 "ESP6500_EA_AF",
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181 "ExAC_AC",
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182 "ExAC_AF",
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183 "ExAC_Adj_AC",
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184 "ExAC_Adj_AF",
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185 "ExAC_AFR_AC",
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186 "ExAC_AFR_AF",
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187 "ExAC_AMR_AC",
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188 "ExAC_AMR_AF",
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189 "ExAC_EAS_AC",
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190 "ExAC_EAS_AF",
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191 "ExAC_FIN_AC",
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192 "ExAC_FIN_AF",
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193 "ExAC_NFE_AC",
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194 "ExAC_NFE_AF",
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195 "ExAC_SAS_AC",
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196 "ExAC_SAS_AF",
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197 "ExAC_nonTCGA_AC",
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198 "ExAC_nonTCGA_AF",
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199 "ExAC_nonTCGA_Adj_AC",
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200 "ExAC_nonTCGA_Adj_AF",
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201 "ExAC_nonTCGA_AFR_AC",
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202 "ExAC_nonTCGA_AFR_AF",
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203 "ExAC_nonTCGA_AMR_AC",
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204 "ExAC_nonTCGA_AMR_AF",
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205 "ExAC_nonTCGA_EAS_AC",
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206 "ExAC_nonTCGA_EAS_AF",
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207 "ExAC_nonTCGA_FIN_AC",
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208 "ExAC_nonTCGA_FIN_AF",
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209 "ExAC_nonTCGA_NFE_AC",
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210 "ExAC_nonTCGA_NFE_AF",
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211 "ExAC_nonTCGA_SAS_AC",
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212 "ExAC_nonTCGA_SAS_AF",
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213 "ExAC_nonpsych_AC",
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214 "ExAC_nonpsych_AF",
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215 "ExAC_nonpsych_Adj_AC",
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216 "ExAC_nonpsych_Adj_AF",
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217 "ExAC_nonpsych_AFR_AC",
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218 "ExAC_nonpsych_AFR_AF",
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219 "ExAC_nonpsych_AMR_AC",
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220 "ExAC_nonpsych_AMR_AF",
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221 "ExAC_nonpsych_EAS_AC",
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222 "ExAC_nonpsych_EAS_AF",
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223 "ExAC_nonpsych_FIN_AC",
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224 "ExAC_nonpsych_FIN_AF",
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225 "ExAC_nonpsych_NFE_AC",
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226 "ExAC_nonpsych_NFE_AF",
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227 "ExAC_nonpsych_SAS_AC",
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228 "ExAC_nonpsych_SAS_AF",
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229 "gnomAD_exomes_AC",
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230 "gnomAD_exomes_AN",
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231 "gnomAD_exomes_AF",
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232 "gnomAD_exomes_AFR_AC",
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233 "gnomAD_exomes_AFR_AN",
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234 "gnomAD_exomes_AFR_AF",
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235 "gnomAD_exomes_AMR_AC",
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236 "gnomAD_exomes_AMR_AN",
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237 "gnomAD_exomes_AMR_AF",
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238 "gnomAD_exomes_ASJ_AC",
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239 "gnomAD_exomes_ASJ_AN",
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240 "gnomAD_exomes_ASJ_AF",
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241 "gnomAD_exomes_EAS_AC",
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242 "gnomAD_exomes_EAS_AN",
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243 "gnomAD_exomes_EAS_AF",
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244 "gnomAD_exomes_FIN_AC",
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245 "gnomAD_exomes_FIN_AN",
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246 "gnomAD_exomes_FIN_AF",
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247 "gnomAD_exomes_NFE_AC",
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248 "gnomAD_exomes_NFE_AN",
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249 "gnomAD_exomes_NFE_AF",
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250 "gnomAD_exomes_SAS_AC",
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251 "gnomAD_exomes_SAS_AN",
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252 "gnomAD_exomes_SAS_AF",
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253 "gnomAD_exomes_OTH_AC",
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254 "gnomAD_exomes_OTH_AN",
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255 "gnomAD_exomes_OTH_AF",
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256 "gnomAD_genomes_AC",
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257 "gnomAD_genomes_AN",
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258 "gnomAD_genomes_AF",
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259 "gnomAD_genomes_AFR_AC",
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260 "gnomAD_genomes_AFR_AN",
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261 "gnomAD_genomes_AFR_AF",
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262 "gnomAD_genomes_AMR_AC",
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263 "gnomAD_genomes_AMR_AN",
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264 "gnomAD_genomes_AMR_AF",
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265 "gnomAD_genomes_ASJ_AC",
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266 "gnomAD_genomes_ASJ_AN",
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267 "gnomAD_genomes_ASJ_AF",
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268 "gnomAD_genomes_EAS_AC",
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269 "gnomAD_genomes_EAS_AN",
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270 "gnomAD_genomes_EAS_AF",
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271 "gnomAD_genomes_FIN_AC",
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272 "gnomAD_genomes_FIN_AN",
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273 "gnomAD_genomes_FIN_AF",
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274 "gnomAD_genomes_NFE_AC",
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275 "gnomAD_genomes_NFE_AN",
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276 "gnomAD_genomes_NFE_AF",
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277 "gnomAD_genomes_OTH_AC",
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278 "gnomAD_genomes_OTH_AN",
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279 "gnomAD_genomes_OTH_AF",
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280 "clinvar_rs",
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281 "clinvar_clnsig",
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282 "clinvar_trait",
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283 "clinvar_golden_stars",
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284 "Interpro_domain",
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285 "GTEx_V6p_gene",
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286 "GTEx_V6p_tissue"
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287 ],
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288 },
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289 ]
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290 },
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291
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292 # CADD
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293 # https://github.com/ensembl-variation/VEP_plugins/blob/master/CADD.pm
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294 # Requires tabix-indexed data file as first param
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295 # No other parameters so no form required
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296 # data file currently only available for GRCh37
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297 {
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298 "key" => "CADD",
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299 "label" => "CADD",
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300 "available" => 0,
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301 "enabled" => 0,
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302 "section" => "Pathogenicity predictions",
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303 "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.",
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304 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/CADD.pm",
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305 "requires_data" => 1,
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306 "species" => [
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307 "homo_sapiens"
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308 ],
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309 "params" => [
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310 #"/path/to/whole_genome_SNVs.tsv.gz"
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311 ]
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312 },
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313
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314 # FATHMM-MKL
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315 # https://github.com/ensembl-variation/VEP_plugins/blob/master/FATHMM_MKL.pm
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316 # Requires tabix-indexed data file as first param
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317 # No other parameters so no form required
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318 # data file currently only available for GRCh37
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319 {
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320 "key" => "FATHMM_MKL",
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321 "label" => "FATHMM-MKL",
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322 "available" => 0,
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323 "enabled" => 0,
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324 "section" => "Pathogenicity predictions",
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325 "helptip" => "FATHMM-MKL predicts functional consequences of variants, both coding and non-coding.",
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326 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/FATHMM_MKL.pm",
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327 "requires_data" => 1,
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328 "species" => [
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329 "homo_sapiens"
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330 ],
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331 "params" => [
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332 #"/path/to/fathmm-MKL_Current.tab.gz"
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333 ]
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334 },
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335
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336 # GWAVA
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337 # https://www.sanger.ac.uk/sanger/StatGen_Gwava
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338 # Requires tabix-indexed BED data file from ftp://ftp.sanger.ac.uk/pub/resources/software/gwava/v1.0/VEP_plugin/
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339 # data file currently only available for GRCh37
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340 {
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341 "key" => "Gwava",
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342 "label" => "GWAVA",
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343 "available" => 0,
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344 "enabled" => 0,
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345 "section" => "Pathogenicity predictions",
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346 "helptip" => "Retrieves precomputed Genome Wide Annotation of VAriants (GWAVA) scores for any variant that overlaps a known variant from the Ensembl variation database",
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347 "plugin_url" => "ftp://ftp.sanger.ac.uk/pub/resources/software/gwava/v1.0/VEP_plugin/Gwava.pm",
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348 "requires_data" => 1,
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349 "species" => [
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350 "homo_sapiens"
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351 ],
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352 "params" => [
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353 "@*",
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354 # "/path/to/gwava_scores.bed.gz"
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355 ],
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356 "form" => [
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357 {
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358 "name" => "model",
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359 "label" => "Model",
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360 "type" => "dropdown",
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361 "values" => [
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362 { "value" => "region", "caption" => "Region" },
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363 { "value" => "tss", "caption" => "TSS" },
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364 { "value" => "unmatched", "caption" => "Unmatched" }
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365 ],
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366 "value" => "region",
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367 },
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368 ],
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369 },
|
|
|
370
|
|
|
371 # Carol
|
|
|
372 # https://github.com/ensembl-variation/VEP_plugins/blob/master/Carol.pm
|
|
|
373 # Requires Math/CDF Perl module
|
|
|
374 {
|
|
|
375 "key" => "Carol",
|
|
|
376 "helptip" => "Calculates the Combined Annotation scoRing toOL (CAROL) score for a missense mutation based on the pre-calculated SIFT and PolyPhen scores",
|
|
|
377 "available" => 0,
|
|
|
378 "enabled" => 0,
|
|
|
379 "section" => "Pathogenicity predictions",
|
|
|
380 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/Carol.pm",
|
|
|
381 "requires_install" => 1,
|
|
|
382 "species" => [
|
|
|
383 "homo_sapiens"
|
|
|
384 ],
|
|
|
385 },
|
|
|
386
|
|
|
387 # Condel
|
|
|
388 # https://github.com/ensembl-variation/VEP_plugins/blob/master/Condel.pm
|
|
|
389 # Requires path to config directory as first param
|
|
|
390 # config directory is checked out as part of VEP_plugins repo, as /[path]/VEP_plugins/config/Condel/config
|
|
|
391 # Within that dir, edit condel_SP.conf so that condel.dir points to /[path]/VEP_plugins/config/Condel
|
|
|
392 {
|
|
|
393 "key" => "Condel",
|
|
|
394 "helptip" => "Calculates the Consensus Deleteriousness (Condel) score for a missense mutation based on the pre-calculated SIFT and PolyPhen scores",
|
|
|
395 "available" => 0,
|
|
|
396 "enabled" => 0,
|
|
|
397 "section" => "Pathogenicity predictions",
|
|
|
398 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/Condel.pm",
|
|
|
399 "requires_install" => 1,
|
|
|
400 "species" => [
|
|
|
401 "homo_sapiens"
|
|
|
402 ],
|
|
|
403 "params" => [
|
|
|
404 # "/path/to/config/Condel/config",
|
|
|
405 "@*"
|
|
|
406 ],
|
|
|
407 "form" => [
|
|
|
408 {
|
|
|
409 "name" => "score_pred",
|
|
|
410 "label" => "Score/prediction",
|
|
|
411 "type" => "dropdown",
|
|
|
412 "values" => [
|
|
|
413 { "value" => "b", "caption" => "Prediction and score" },
|
|
|
414 { "value" => "p", "caption" => "Prediction only" },
|
|
|
415 { "value" => "s", "caption" => "Score only" }
|
|
|
416 ],
|
|
|
417 "value" => "b",
|
|
|
418 },
|
|
|
419 ],
|
|
|
420 },
|
|
|
421
|
|
|
422 # LOFTEE
|
|
|
423 # See https://github.com/konradjk/loftee for details
|
|
|
424 {
|
|
|
425 "key" => "LoF",
|
|
|
426 "helptip" => "LOFTEE identifies LoF (loss-of-function) variation",
|
|
|
427 "available" => 0,
|
|
|
428 "enabled" => 0,
|
|
|
429 "section" => "Pathogenicity predictions",
|
|
|
430 "plugin_url" => "https://raw.githubusercontent.com/konradjk/loftee/master/LoF.pm",
|
|
|
431 "requires_data" => 1,
|
|
|
432 "requires_install" => 1,
|
|
|
433 "params" => [
|
|
|
434 "@*"
|
|
|
435 ]
|
|
|
436 },
|
|
|
437
|
|
|
438 # LoFtool
|
|
|
439 # Requires LoFtool_scores.txt file as first param (available in VEP_plugins GitHub repo)
|
|
|
440 {
|
|
|
441 "key" => "LoFtool",
|
|
|
442 "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",
|
|
|
443 "available" => 0,
|
|
|
444 "enabled" => 0,
|
|
|
445 "section" => "Pathogenicity predictions",
|
|
|
446 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/LoFtool.pm",
|
|
|
447 "requires_data" => 1,
|
|
|
448 "species" => [
|
|
|
449 "homo_sapiens"
|
|
|
450 ],
|
|
|
451 "params" => [
|
|
|
452 # "/path/to/LoFtool_scores.txt"
|
|
|
453 ]
|
|
|
454 },
|
|
|
455
|
|
|
456 # ExACpLI
|
|
|
457 # Requires ExACpLI_values.txt file as first param (available in VEP_plugins GitHub repo)
|
|
|
458 {
|
|
|
459 "key" => "ExACpLI",
|
|
|
460 "helptip" => "Provides a per-gene probability of being loss-of-function intolerant (pLI) from ExAC data",
|
|
|
461 "available" => 0,
|
|
|
462 "enabled" => 0,
|
|
|
463 "section" => "Pathogenicity predictions",
|
|
|
464 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/ExACpLI.pm",
|
|
|
465 "requires_data" => 1,
|
|
|
466 "species" => [
|
|
|
467 "homo_sapiens"
|
|
|
468 ],
|
|
|
469 "params" => [
|
|
|
470 # "/path/to/ExACpLI_values.txt"
|
|
|
471 ]
|
|
|
472 },
|
|
|
473
|
|
|
474 # MPC
|
|
|
475 # Requires fordist_constraint_official_mpc_values.txt.gz data file
|
|
|
476 {
|
|
|
477 "key" => "MPC",
|
|
|
478 "helptip" => "MPC is a missense deleteriousness metric based on the analysis of genic regions depleted of missense mutations in ExAC",
|
|
|
479 "available" => 0,
|
|
|
480 "enabled" => 0,
|
|
|
481 "section" => "Pathogenicity predictions",
|
|
|
482 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/MPC.pm",
|
|
|
483 "requires_data" => 1,
|
|
|
484 "species" => [
|
|
|
485 "homo_sapiens"
|
|
|
486 ],
|
|
|
487 "params" => [
|
|
|
488 # "/path/to/fordist_constraint_official_mpc_values.txt.gz"
|
|
|
489 ]
|
|
|
490 },
|
|
|
491
|
|
|
492 # MTR
|
|
|
493 # Requires mtrflatfile_1.0.txt.gz data file from ftp://mtr-viewer.mdhs.unimelb.edu.au/pub
|
|
|
494 {
|
|
|
495 "key" => "MTR",
|
|
|
496 "helptip" => "MTR scores quantify the amount of purifying selection acting specifically on missense variants in a given window of protein-coding sequence",
|
|
|
497 "available" => 0,
|
|
|
498 "enabled" => 0,
|
|
|
499 "section" => "Pathogenicity predictions",
|
|
|
500 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/MTR.pm",
|
|
|
501 "requires_data" => 1,
|
|
|
502 "species" => [
|
|
|
503 "homo_sapiens"
|
|
|
504 ],
|
|
|
505 "params" => [
|
|
|
506 # "/path/to/mtrflatfile_1.0.txt.gz"
|
|
|
507 ]
|
|
|
508 },
|
|
|
509
|
|
|
510 # REVEL
|
|
|
511 # Requires data file processed from revel_all_chromosomes.csv.zip
|
|
|
512 {
|
|
|
513 "key" => "REVEL",
|
|
|
514 "helptip" => "An ensemble method for predicting the pathogenicity of rare missense variants",
|
|
|
515 "available" => 0,
|
|
|
516 "enabled" => 0,
|
|
|
517 "section" => "Pathogenicity predictions",
|
|
|
518 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/REVEL.pm",
|
|
|
519 "requires_data" => 1,
|
|
|
520 "species" => [
|
|
|
521 "homo_sapiens"
|
|
|
522 ],
|
|
|
523 "params" => [
|
|
|
524 # "/path/to/revel_all_chromosomes.tsv.gz"
|
|
|
525 ]
|
|
|
526 },
|
|
|
527
|
|
|
528
|
|
|
529
|
|
|
530 ## SPLICING PREDICTIONS
|
|
|
531 #######################
|
|
|
532
|
|
|
533 # dbscSNV
|
|
|
534 {
|
|
|
535 "key" => "dbscSNV",
|
|
|
536 "label" => "dbscSNV",
|
|
|
537 "available" => 0,
|
|
|
538 "enabled" => 0,
|
|
|
539 "section" => "Splicing predictions",
|
|
|
540 "helptip" => "Retrieves data for splicing variants from a tabix-indexed dbscSNV file",
|
|
|
541 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/dbscSNV.pm",
|
|
|
542 "requires_data" => 1,
|
|
|
543 "requires_install" => 1,
|
|
|
544 "params" => [
|
|
|
545 #"/path/to/dbscSNV1.1.txt.gz"
|
|
|
546 ],
|
|
|
547 "species" => [
|
|
|
548 "homo_sapiens"
|
|
|
549 ],
|
|
|
550 },
|
|
|
551
|
|
|
552 # GeneSplicer
|
|
|
553 {
|
|
|
554 "key" => "GeneSplicer",
|
|
|
555 "label" => "GeneSplicer",
|
|
|
556 "helptip" => "Detects splice sites in genomic DNA",
|
|
|
557 "available" => 0,
|
|
|
558 "enabled" => 0,
|
|
|
559 "section" => "Splicing predictions",
|
|
|
560 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/GeneSplicer.pm",
|
|
|
561 "requires_install" => 1,
|
|
|
562 "species" => [
|
|
|
563 "homo_sapiens"
|
|
|
564 ],
|
|
|
565 "params" => [
|
|
|
566 #"/path/to/genesplicer/bin/linux/genesplicer",
|
|
|
567 #"/path/to/genesplicer/human",
|
|
|
568 "@*"
|
|
|
569 ]
|
|
|
570 },
|
|
|
571
|
|
|
572 # MaxEntScan
|
|
|
573 {
|
|
|
574 "key" => "MaxEntScan",
|
|
|
575 "label" => "MaxEntScan",
|
|
|
576 "helptip" => "Sequence motif and maximum entropy based splice site consensus predictions",
|
|
|
577 "available" => 0,
|
|
|
578 "enabled" => 0,
|
|
|
579 "section" => "Splicing predictions",
|
|
|
580 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/MaxEntScan.pm",
|
|
|
581 "requires_install" => 1,
|
|
|
582 "species" => [
|
|
|
583 "homo_sapiens"
|
|
|
584 ],
|
|
|
585 "params" => [
|
|
|
586 #"/path/to/maxentscan"
|
|
|
587 ]
|
|
|
588 },
|
|
|
589
|
|
|
590 # SpliceRegion
|
|
|
591 {
|
|
|
592 "key" => "SpliceRegion",
|
|
|
593 "label" => "SpliceRegion",
|
|
|
594 "helptip" => "More granular predictions of splicing effects",
|
|
|
595 "available" => 0,
|
|
|
596 "enabled" => 0,
|
|
|
597 "section" => "Splicing predictions",
|
|
|
598 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/SpliceRegion.pm",
|
|
|
599 },
|
|
|
600
|
|
|
601
|
|
|
602 ## CONSERVATION
|
|
|
603 ###############
|
|
|
604
|
|
|
605 # Blosum62
|
|
|
606 {
|
|
|
607 "key" => "Blosum62",
|
|
|
608 "label" => "BLOSUM62",
|
|
|
609 "helptip" => "BLOSUM62 amino acid conservation score",
|
|
|
610 "available" => 0,
|
|
|
611 "enabled" => 0,
|
|
|
612 "section" => "Conservation",
|
|
|
613 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/Blosum62.pm",
|
|
|
614 },
|
|
|
615
|
|
|
616 # Conservation
|
|
|
617 # Use the following query to get valid species sets:
|
|
|
618 #
|
|
|
619 # SELECT group_concat(concat("_stt_", gd.name) SEPARATOR ' '), REPLACE(mlss.name, "Gerp Conservation Scores ", ""), sst.value
|
|
|
620 # FROM method_link ml,
|
|
|
621 # method_link_species_set mlss,
|
|
|
622 # genome_db gd, species_set ss, species_set_tag sst
|
|
|
623 # WHERE mlss.method_link_id = ml.method_link_id AND
|
|
|
624 # mlss.species_set_id = ss.species_set_id AND
|
|
|
625 # ss.genome_db_id = gd.genome_db_id AND
|
|
|
626 # ss.species_set_id = sst.species_set_id AND
|
|
|
627 # (ml.class = "ConservationScore.conservation_score")
|
|
|
628 # GROUP BY mlss.species_set_id
|
|
|
629 {
|
|
|
630 "key" => "Conservation",
|
|
|
631 "helptip" => "Retrieves a conservation score from the Ensembl Compara databases for variant positions",
|
|
|
632 "available" => 0,
|
|
|
633 "enabled" => 0,
|
|
|
634 "section" => "Conservation",
|
|
|
635 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/Conservation.pm",
|
|
|
636 "params" => [
|
|
|
637 "@*"
|
|
|
638 ],
|
|
|
639 "form" => [
|
|
|
640 {
|
|
|
641 "name" => "method_link_type",
|
|
|
642 "label" => "Method",
|
|
|
643 "type" => "dropdown",
|
|
|
644 "values" => [
|
|
|
645 { "value" => "GERP_CONSERVATION_SCORE", "caption" => "GERP"}
|
|
|
646 ]
|
|
|
647 },
|
|
|
648 {
|
|
|
649 "name" => "species_set",
|
|
|
650 "label" => "Species set",
|
|
|
651 "type" => "dropdown",
|
|
|
652 "values" => [
|
|
|
653 { "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" },
|
|
|
654 { "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" },
|
|
|
655 { "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" },
|
|
|
656 { "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" },
|
|
|
657 ]
|
|
|
658 },
|
|
|
659 ]
|
|
|
660 },
|
|
|
661
|
|
|
662 # AncestralAllele
|
|
|
663 # Requires processed FASTA file from ftp://ftp.ensembl.org/pub/current_fasta/ancestral_alleles/
|
|
|
664 {
|
|
|
665 "key" => "AncestralAllele",
|
|
|
666 "label" => "Ancestral allele",
|
|
|
667 "helptip" => "Retrieves the ancestral allele for variants inferred from the Ensembl Compara Enredo-Pecan-Ortheus (EPO) pipeline",
|
|
|
668 "available" => 0,
|
|
|
669 "enabled" => 0,
|
|
|
670 "section" => "Conservation",
|
|
|
671 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/AncestralAllele.pm",
|
|
|
672 "requires_data" => 1,
|
|
|
673 "species" => [
|
|
|
674 "homo_sapiens"
|
|
|
675 ],
|
|
|
676 "params" => [
|
|
|
677 # "/path/to/homo_sapiens_ancestor_GRCh38_e93.fa.gz"
|
|
|
678 ]
|
|
|
679 },
|
|
|
680
|
|
|
681
|
|
|
682 ## FREQUENCY DATA
|
|
|
683 #################
|
|
|
684
|
|
|
685 # ExAC
|
|
|
686 {
|
|
|
687 "key" => "ExAC",
|
|
|
688 "label" => "ExAC frequencies",
|
|
|
689 "helptip" => "Reports allele frequencies from the Exome Aggregation Consortium",
|
|
|
690 "available" => 0,
|
|
|
691 "enabled" => 0,
|
|
|
692 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/ExAC.pm",
|
|
|
693 "section" => "Frequency data",
|
|
|
694 "requires_data" => 1,
|
|
|
695 "species" => [
|
|
|
696 "homo_sapiens"
|
|
|
697 ],
|
|
|
698 "params" => [
|
|
|
699 # "/path/to/ExAC.r0.3.sites.vep.vcf.gz"
|
|
|
700 ]
|
|
|
701 },
|
|
|
702
|
|
|
703
|
|
|
704 ## OTHER
|
|
|
705 ########
|
|
|
706
|
|
|
707 # CSN
|
|
|
708 {
|
|
|
709 "key" => "CSN",
|
|
|
710 "helptip" => "Reports Clinical Sequencing Nomenclature (CSN) for variants",
|
|
|
711 "available" => 0,
|
|
|
712 "enabled" => 0,
|
|
|
713 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/CSN.pm",
|
|
|
714 },
|
|
|
715
|
|
|
716 # miRNA
|
|
|
717 {
|
|
|
718 "key" => "miRNA",
|
|
|
719 "label" => "miRNA structure",
|
|
|
720 "helptip" => "Determines where in the secondary structure of a miRNA a variant falls",
|
|
|
721 "available" => 0,
|
|
|
722 "enabled" => 0,
|
|
|
723 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/miRNA.pm",
|
|
|
724 },
|
|
|
725
|
|
|
726
|
|
|
727
|
|
|
728 # NearestGene
|
|
|
729 {
|
|
|
730 "key" => "NearestGene",
|
|
|
731 "label" => "Nearest gene",
|
|
|
732 "helptip" => "Finds the nearest gene to non-genic variants",
|
|
|
733 "available" => 0,
|
|
|
734 "enabled" => 0,
|
|
|
735 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/NearestGene.pm",
|
|
|
736 },
|
|
|
737
|
|
|
738 # LD
|
|
|
739 {
|
|
|
740 "key" => "LD",
|
|
|
741 "label" => "Linkage disequilibrium",
|
|
|
742 "helptip" => "Finds variants in linkage disequilibrium with any overlapping existing variants from the Ensembl variation databases",
|
|
|
743 "available" => 0,
|
|
|
744 "enabled" => 0,
|
|
|
745 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/LD.pm",
|
|
|
746 "section" => "Variant data",
|
|
|
747 "params" => [
|
|
|
748 "@*"
|
|
|
749 ],
|
|
|
750 "form" => [
|
|
|
751 {
|
|
|
752 "name" => "population",
|
|
|
753 "label" => "Population",
|
|
|
754 "type" => "dropdown",
|
|
|
755 "values" => [
|
|
|
756 { "value" => "1000GENOMES:phase_3:ACB", "caption" => "African Caribbean in Barbados" },
|
|
|
757 { "value" => "1000GENOMES:phase_3:ASW", "caption" => "African Ancestry in Southwest US" },
|
|
|
758 { "value" => "1000GENOMES:phase_3:BEB", "caption" => "Bengali in Bangladesh" },
|
|
|
759 { "value" => "1000GENOMES:phase_3:CDX", "caption" => "Chinese Dai in Xishuangbanna, China" },
|
|
|
760 { "value" => "1000GENOMES:phase_3:CEU", "caption" => "Utah residents with Northern and Western European ancestry" },
|
|
|
761 { "value" => "1000GENOMES:phase_3:CHB", "caption" => "Han Chinese in Bejing, China" },
|
|
|
762 { "value" => "1000GENOMES:phase_3:CHS", "caption" => "Southern Han Chinese, China" },
|
|
|
763 { "value" => "1000GENOMES:phase_3:CLM", "caption" => "Colombian in Medellin, Colombia" },
|
|
|
764 { "value" => "1000GENOMES:phase_3:ESN", "caption" => "Esan in Nigeria" },
|
|
|
765 { "value" => "1000GENOMES:phase_3:FIN", "caption" => "Finnish in Finland" },
|
|
|
766 { "value" => "1000GENOMES:phase_3:GBR", "caption" => "British in England and Scotland" },
|
|
|
767 { "value" => "1000GENOMES:phase_3:GIH", "caption" => "Gujarati Indian in Houston, TX" },
|
|
|
768 { "value" => "1000GENOMES:phase_3:IBS", "caption" => "Iberian populations in Spain" },
|
|
|
769 { "value" => "1000GENOMES:phase_3:ITU", "caption" => "Indian Telugu in the UK" },
|
|
|
770 { "value" => "1000GENOMES:phase_3:JPT", "caption" => "Japanese in Tokyo, Japan" },
|
|
|
771 { "value" => "1000GENOMES:phase_3:KHV", "caption" => "Kinh in Ho Chi Minh City, Vietnam" },
|
|
|
772 { "value" => "1000GENOMES:phase_3:LWK", "caption" => "Luhya in Webuye, Kenya" },
|
|
|
773 { "value" => "1000GENOMES:phase_3:MAG", "caption" => "Mandinka in The Gambia" },
|
|
|
774 { "value" => "1000GENOMES:phase_3:MSL", "caption" => "Mende in Sierra Leone" },
|
|
|
775 { "value" => "1000GENOMES:phase_3:MXL", "caption" => "Mexican Ancestry in Los Angeles, California" },
|
|
|
776 { "value" => "1000GENOMES:phase_3:PEL", "caption" => "Peruvian in Lima, Peru" },
|
|
|
777 { "value" => "1000GENOMES:phase_3:PJL", "caption" => "Punjabi in Lahore, Pakistan" },
|
|
|
778 { "value" => "1000GENOMES:phase_3:PUR", "caption" => "Puerto Rican in Puerto Rico" },
|
|
|
779 { "value" => "1000GENOMES:phase_3:STU", "caption" => "Sri Lankan Tamil in the UK" },
|
|
|
780 { "value" => "1000GENOMES:phase_3:TSI", "caption" => "Toscani in Italy" },
|
|
|
781 { "value" => "1000GENOMES:phase_3:YRI", "caption" => "Yoruba in Ibadan, Nigeria" },
|
|
|
782 ],
|
|
|
783 "value" => "1000GENOMES:phase_3:CEU",
|
|
|
784 },
|
|
|
785 {
|
|
|
786 "name" => "threshold",
|
|
|
787 "label" => "r2 cutoff",
|
|
|
788 "type" => "string",
|
|
|
789 "value" => 0.8,
|
|
|
790 },
|
|
|
791 ]
|
|
|
792 },
|
|
|
793
|
|
|
794 # SameCodon
|
|
|
795 {
|
|
|
796 "key" => "SameCodon",
|
|
|
797 "label" => "Variants in same codon",
|
|
|
798 "helptip" => "Reports existing variants that fall in the same codon",
|
|
|
799 "available" => 0,
|
|
|
800 "enabled" => 0,
|
|
|
801 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/SameCodon.pm",
|
|
|
802 "section" => "Variant data",
|
|
|
803 },
|
|
|
804 # LOVD
|
|
|
805 {
|
|
|
806 "key" => "LOVD",
|
|
|
807 "label" => "LOVD",
|
|
|
808 "helptip" => "Retrieves LOVD variation data",
|
|
|
809 "available" => 0,
|
|
|
810 "enabled" => 0,
|
|
|
811 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/LOVD.pm",
|
|
|
812 "section" => "Variant data",
|
|
|
813 },
|
|
|
814
|
|
|
815 # GO
|
|
|
816 {
|
|
|
817 "key" => "GO",
|
|
|
818 "label" => "Gene Ontology",
|
|
|
819 "helptip" => "Retrieves Gene Ontology terms associated with transcripts/translations via the Ensembl API",
|
|
|
820 "available" => 0,
|
|
|
821 "enabled" => 0,
|
|
|
822 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/GO.pm",
|
|
|
823 "section" => "Gene data",
|
|
|
824 },
|
|
|
825
|
|
|
826 # Downstream
|
|
|
827 {
|
|
|
828 "key" => "Downstream",
|
|
|
829 "label" => "Downstream",
|
|
|
830 "helptip" => "Predicts the downstream effects of a frameshift variant on the protein sequence of a transcript",
|
|
|
831 "available" => 0,
|
|
|
832 "enabled" => 0,
|
|
|
833 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/Downstream.pm",
|
|
|
834 },
|
|
|
835
|
|
|
836 # ProteinSeqs
|
|
|
837 {
|
|
|
838 "key" => "ProteinSeqs",
|
|
|
839 "label" => "Protein sequences",
|
|
|
840 "helptip" => "Prints out the reference and mutated protein sequences of any proteins found with non-synonymous mutations",
|
|
|
841 "available" => 0,
|
|
|
842 "enabled" => 0,
|
|
|
843 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/ProteinSeqs.pm",
|
|
|
844 },
|
|
|
845
|
|
|
846 # TSSDistance
|
|
|
847 {
|
|
|
848 "key" => "TSSDistance",
|
|
|
849 "label" => "TSS distance",
|
|
|
850 "helptip" => "Calculates the distance from the transcription start site for upstream variants ",
|
|
|
851 "available" => 0,
|
|
|
852 "enabled" => 0,
|
|
|
853 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/TSSDistance.pm",
|
|
|
854 },
|
|
|
855
|
|
|
856 # Phenotypes
|
|
|
857 {
|
|
|
858 "key" => "Phenotypes",
|
|
|
859 "label" => "Phenotypes",
|
|
|
860 "helptip" => "Retrieves overlapping phenotype annotations",
|
|
|
861 "available" => 0,
|
|
|
862 "enabled" => 0,
|
|
|
863 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/Phenotypes.pm",
|
|
|
864 },
|
|
|
865 # Draw
|
|
|
866 {
|
|
|
867 "key" => "Draw",
|
|
|
868 "label" => "Draw",
|
|
|
869 "helptip" => "Creates images of the transcript model showing variant location",
|
|
|
870 "available" => 0,
|
|
|
871 "enabled" => 0,
|
|
|
872 "requires_install" => 1,
|
|
|
873 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/Draw.pm",
|
|
|
874 },
|
|
|
875 # G2P
|
|
|
876 {
|
|
|
877 "key" => "G2P",
|
|
|
878 "label" => "G2P",
|
|
|
879 "helptip" => "Assesses variants using G2P allelic requirements for potential phenotype involvement.",
|
|
|
880 "available" => 0,
|
|
|
881 "enabled" => 0,
|
|
|
882 "requires_data" => 1,
|
|
|
883 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/G2P.pm",
|
|
|
884 },
|
|
|
885
|
|
|
886 # LocalID
|
|
|
887 {
|
|
|
888 "key" => "LocalID",
|
|
|
889 "label" => "LocalID",
|
|
|
890 "helptip" => "Allows you to use variant IDs as VEP input without making a database connection.",
|
|
|
891 "available" => 0,
|
|
|
892 "enabled" => 0,
|
|
|
893 "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/94/LocalID.pm",
|
|
|
894 },
|
|
|
895
|
|
|
896
|
|
|
897 ]
|
|
|
898 };
|
