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1 ############################
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2 # #
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3 # Variant Effect Predictor #
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4 # #
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5 ############################
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6
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7 Copyright (c) 1999-2011 The European Bioinformatics Institute and
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8 Genome Research Limited. All rights reserved.
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9
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10 This software is distributed under a modified Apache license.
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11 For license details, please see
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12
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13 http://www.ensembl.org/info/about/code_licence.html
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14
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15 Please email comments or questions to the public Ensembl
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16 developers list at <dev@ensembl.org>.
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17
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18 Questions may also be sent to the Ensembl help desk at
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19 <helpdesk@ensembl.org>
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20
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21 Quickstart
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22 ==========
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23
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24 Install API and cache files, run in offline mode:
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25
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26 perl INSTALL.pl
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27 perl variant_effect_predictor.pl --offline
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28
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29
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30 Documentation
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31 =============
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32
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33 For a summary of command line flags, run:
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34
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35 perl variant_effect_predictor.pl --help
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36
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37 For full documentation see
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38
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39 http://www.ensembl.org/info/docs/variation/vep/vep_script.html
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40
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41
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42
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43 Changelog
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44 =========
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45
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46 New in version 2.6 (July 2012)
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47 ------------------------------
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48
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49 - support for structural variant consequences
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50
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51 - Sequence Ontology (SO) consequence terms now default
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52
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53 - script runtime 3-4x faster when using forking
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54
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55 - 1000 Genomes global MAF available in cache files
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56
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57 - improved memory usage
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58
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59
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60 New in version 2.5 (May 2012)
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61 -----------------------------
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62
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63 - SIFT and PolyPhen predictions now available for RefSeq transcripts
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64
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65 - retrieve cell type-specific regulatory consequences
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66
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67 - consequences can be retrieved based on a single individual's genotype in
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68 a VCF input file
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69
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70 - find overlapping structural variants
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71
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72 - Condel support removed from main script and moved to a plugin
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73
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74
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75 New in version 2.4 (February 2012)
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76 ----------------------------------
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77 - offline mode and new installer script make it easy to use the VEP without
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78 the usual dependencies
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79
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80 - output columns configurable using the --fields flag
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81
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82 - VCF output support expanded, can now carry all fields
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83
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84 - output affected exon and intron numbers with --numbers
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85
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86 - output overlapping protein domains using --domains
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87
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88 - enhanced support for LRGs
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89
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90 - plugins now work on variants called as intergenic
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91
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92
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93 New in version 2.3 (December 2011)
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94 ----------------------------------
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95
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96 - Add custom annotations from tabix-indexed files (BED, GFF, GTF, VCF, bigWig)
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97
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98 - Add new functionality to the VEP with user-written plugins
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99
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100 - Filter input on consequence type
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101
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102
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103 Version 2.2 (September 2011)
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104 ----------------------------
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105
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106 - SIFT, PolyPhen and Condel predictions and regulatory features now accessible
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107 from the cache
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108
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109 - Support for calling consequences against RefSeq transcripts
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110
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111 - Variant identifiers (e.g. dbSNP rsIDs) and HGVS notations supported as input
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112 format
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113
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114 - Variants can now be filtered by frequency in HapMap and 1000 genomes
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115 populations
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116
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117 - Script can be used to convert files between formats (Ensembl/VCF/Pileup/HGVS
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118 to Ensembl/VCF/Pileup)
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119
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120 - Large amount of code moved to API modules to ensure consistency between web
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121 and script VEP
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122
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123 - Memory usage optimisations
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124
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125 - VEP script moved to ensembl-tools CVS module
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126
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127 - Added --canonical, --per_gene and --no_intergenic options
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128
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129
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130 Version 2.1 (June 2011)
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131 -----------------------
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132
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133 - ability to use local file cache in place of or alongside connecting to an
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134 Ensembl database
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135
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136 - significant improvements to speed of script
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137
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138 - whole-genome mode now default (no disadvantage for smaller datasets)
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139
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140 - improved status output with progress bars
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141
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142 - regulatory region consequences now reinstated and improved
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143
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144 - modification to output file - Transcript column is now Feature, and is
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145 followed by a Feature_type column
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146
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147 - full documentation now online
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148
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149
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150 Version 2.0 (April 2011)
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151 ------------------------
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152
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153 Version 2.0 of the Variant Effect Predictor script (VEP) constitutes a complete
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154 overhaul of both the script and the API behind it. It requires at least version
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155 62 of the Ensembl API to function. Here follows a summary of the changes:
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156
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157 - support for SIFT, PolyPhen and Condel non-synonymous predictions in human
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158
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159 - per-allele and compound consequence types
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160
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161 - support for Sequence Ontology (SO) and NCBI consequence terms
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162
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163 - modified output format
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164 - support for new output fields in Extra column
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165 - header section containing information on database and software versions
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166 - codon change shown in output
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167 - CDS position shown in output
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168 - option to output Ensembl protein identifiers
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169 - option to output HGVS nomenclature for variants
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170
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171 - support for gzipped input files
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172
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173 - enhanced configuration options, including the ability to read configuration
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174 from a file
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175
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176 - verbose output now much more useful
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177
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178 - whole-genome mode now more stable
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179
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180 - finding existing co-located variations now ~5x faster
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