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1 <tool id="sniplay_vcf2fastaandhapmap" name="VCF to Hapmap" version="1.1.0">
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2
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3 <!-- [REQUIRED] Tool description displayed after the tool name -->
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4 <description> Convert VCF to Hapmap </description>
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5
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6 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
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7 <requirements>
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8 <requirement type="binary">perl</requirement>
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9 </requirements>
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10
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11 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
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12 <stdio>
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13 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
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14 <exit_code range="1:" level="fatal" />
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15 </stdio>
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16
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17 <!-- [OPTIONAL] Command to be executed to get the tool's version string -->
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18 <version_command>
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19 <!--
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20 tool_binary -v
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21 -->
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22 </version_command>
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23
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24 <!-- [REQUIRED] The command to execute -->
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25 <command interpreter="bash">
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26 vcf2FastaAndHapmap.sh $filein $fileout $optional.file_opt
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27 #if str( $optional.file_opt ) != "none":
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28 $fileout_seq $fileout_fa1 $filefasta
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29 #if str( $optional.file_opt ) == "fasta_gff":
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30 $filegff
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31 #end if
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32 #end if
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33 </command>
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34
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35 <!-- [REQUIRED] Input files and tool parameters -->
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36 <inputs>
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37 <param name="filein" type="data" format="vcf" optional="false" label="VCF input" />
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38 <param name="fileout_label" type="text" value="input" optional="false" label="Output file basename"/>
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39 <conditional name="optional" >
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40 <param name="file_opt" type="select" label="Optional files" >
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41 <option value="none" selected="true">No</option>
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42 <option value="fasta">Fasta</option>
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43 <option value="fasta_gff">Fasta and GFF</option>
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44 </param>
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45 <when value="none" />
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46 <when value="fasta">
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47 <param name="filefasta" type="data" format="fasta" optional="false" label="Fasta file input" />
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48 </when>
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49 <when value="fasta_gff">
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50 <param name="filefasta" type="data" format="fasta" optional="false" label="Fasta file input" />
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51 <param name="filegff" type="data" format="gff" optional="false" label="GFF file input" help="VCF file must be annotated" />
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52 </when>
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53 </conditional>
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54 </inputs>
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55
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56 <!-- [REQUIRED] Output files -->
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57 <outputs>
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58 <data name="fileout" format="txt" label="${fileout_label}.hapmap" />
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59 <data name="fileout_seq" format="txt" label="${fileout_label}.flanking.txt">
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60 <filter>(optional['file_opt'] != 'none')</filter>
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61 </data>
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62 <data name="fileout_fa1" format="fasta" label="${fileout_label}.gene_alignment.fas">
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63 <filter>(optional['file_opt'] == 'fasta_gff')</filter>
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64 </data>
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65 </outputs>
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66
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67 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
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68 <tests>
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69 <!-- [HELP] Test files have to be in the ~/test-data directory -->
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70 <test>
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71 <param name="filein" value="vcf2fastaAndHapmap-sample.vcf" />
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72 <param name="file_opt" value="none" />
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73 <output name="fileout" file="vcf2fastaAndHapmap-result1.hapmap" />
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74 </test>
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75 <test>
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76 <param name="filein" value="vcf2fastaAndHapmap-sample.vcf" />
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77 <param name="file_opt" value="fasta" />
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78 <param name="filefasta" value="vcf2fastaAndHapmap-reference.fa" />
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79 <output name="fileout" file="vcf2fastaAndHapmap-result2.hapmap" />
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80 <output name="fileout_seq" file="vcf2fastaAndHapmap-result2.flanking.txt" />
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81 </test>
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82 <test>
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83 <param name="filein" value="vcf2fastaAndHapmap-sample.vcf" />
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84 <param name="file_opt" value="fasta_gff" />
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85 <param name="filefasta" value="vcf2fastaAndHapmap-reference.fa" />
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86 <param name="filegff" value="vcf2fastaAndHapmap-reference.gff" />
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87 <output name="fileout" file="vcf2fastaAndHapmap-result3.hapmap" />
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88 <output name="fileout_seq" file="vcf2fastaAndHapmap-result3.flanking.txt" />
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89 <output name="fileout_fa1" file="vcf2fastaAndHapmap-result3.gene_alignment.fas" />
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90 </test>
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91 </tests>
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92
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93 <!-- [OPTIONAL] Help displayed in Galaxy -->
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94 <help>
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95
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96
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97 .. class:: infomark
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98
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99 **Authors** Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform
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100
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101 | **Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1).
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102
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103 .. class:: infomark
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104
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105 **Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique.
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106
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107 .. class:: infomark
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108
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109 **Support** For any questions, please send an e-mail to support.abims@sb-roscoff.fr
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110
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111 ---------------------------------------------------
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112
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113 =======================
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114 VCF to Hapmap
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115 =======================
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116
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117 -----------
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118 Description
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119 -----------
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120
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121 | Convert VCF to Hapmap. Additionnaly it creates flanking sequences of variants if fasta reference is provided.
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122 | Furthermore it also creates fasta alignment of genes if GFF annotation is provided
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123
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124 -----------------
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125 Workflow position
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126 -----------------
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127
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128 **Upstream tool**
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129
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130 =============== ========================== =======
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131 Name output file(s) format
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132 =============== ========================== =======
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133 VCFtools Filter VCF file VCF
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134 =============== ========================== =======
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135
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136
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137 **Downstream tool**
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138
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139 =============== ========================== ===========
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140 Name input file(s) format
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141 =============== ========================== ===========
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142 SNP density Hapmap file tabular
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143 =============== ========================== ===========
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144
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145
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146 ----------
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147 Input file
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148 ----------
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149
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150 VCF file
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151 VCF file with all SNPs
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152
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153 ----------
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154 Parameters
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155 ----------
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156
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157 Output file basename
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158 Prefix for the output VCF file
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159
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160 Optional files
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161 To add additional files fasta file and GFF file.
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162
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163 ------------
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164 Output files
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165 ------------
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166
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167 Hapmap file
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168 Hapmap converted file
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169
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170 Additional files
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171 If you add fasta and/or GFF file as reference, you obtain 3 more files : One with flanking sequence and a fasta file
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172
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173 ---------------------------------------------------
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174
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175 ---------------
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176 Working example
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177 ---------------
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178
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179 Input files
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180 ===========
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181
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182 VCF file
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183 ---------
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184
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185 ::
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186
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187 #fileformat=VCFv4.1
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188 #FILTER=<ID=LowQual,Description="Low quality">
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189 #FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
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190 [...]
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191 CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CATB1
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192 chr1 2209 . G T 213.84 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=41.50;MQ0=0;QD=30.55;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,7:7:18:242,18,0
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193
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194 Fasta file
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195 ----------
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196
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197
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198 ::
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199
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200 >chr1
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201 CAGTAAAGTTTGCAAAGAGATTCTGGCAAAGTT
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202
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203 Parameters
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204 ==========
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205
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206 Output name -> input
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207
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208 Optional files -> Fasta
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209
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210
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211 Output files
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212 ============
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213
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214 input.hapmap
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215 ------------
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216
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217 ::
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218
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219 rs# alleles chrom pos strand assembly# center protLSID assayLSID panelLSID QCcode CATB1
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220 chr1:2209 G/T chr1 2209 + NA NA NA NA NA NA GG TT
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221 chr1:2232 A/C chr1 2232 + NA NA NA NA NA NA AA CC
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222
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223 input.flanking.txt
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224 ------------------
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225
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226 ::
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227
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228 chr1-2209,GTCGCATCTGCAGCATATAGCCAACCTTCAACTTGCAGCTAAAACTCATCATCTCTTTCT[G/T]ACTGGCTTAACGATATTGTAAGMTGACTCAGAGGCCCACTTTTTTTTTAAAAATYAGCCT,0,0,0,Project_name,0,diploid,Other,Forward
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229 chr1-2232,ACCTTCAACTTGCAGCTAAAACTCATCATCTCTTTCTKACTGGCTTAACGATATTGTAAG[A/C]TGACTCAGAGGCCCACTTTTTTTTTAAAAATYAGCCTGTCCCCAGCCGTGCTGACTGGGC,0,0,0,Project_name,0,diploid,Other,Forward
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230
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231 input.gene_alignment.fas
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232 ------------------------
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233
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234 ::
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235
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236 >chr1_CATB1_1
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237 TCCTCAAACTTTCTTCAGCGCCTATGAATACAGCGTGCTATAGTTACGTGGGGCGTTT
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238
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239
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240 </help>
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241
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242 <citations>
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243 <!-- [HELP] As DOI or BibTex entry -->
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244 <citation type="bibtex">@article{Dereeper03062015,
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245 author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel},
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246 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},
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247 year = {2015},
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248 doi = {10.1093/nar/gkv351},
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249 abstract ={SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.},
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250 URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract},
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251 eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html},
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252 journal = {Nucleic Acids Research}
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253 }
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254
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255 }</citation>
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256
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257 </citations>
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258
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259 </tool>
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